Class picard.fingerprint.CrosscheckFingerprintsTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null) | 0.009s | passed |
| checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null) | 0.006s | passed |
| checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null) | 0.008s | passed |
| checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null) | 0.005s | passed |
| checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null) | 0.007s | passed |
| checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt) | 0.008s | passed |
| checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt) | 0.008s | passed |
| checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt) | 0.008s | passed |
| testCheckFiles[0]([/tmp/fingerprint14467713583919176379.vcf, /tmp/fingerprint602062117778355363.vcf, /tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint8526523117034821907.vcf], 0, 16, false) | 0.010s | passed |
| testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam], 0, 9, true) | 0.120s | passed |
| testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], 1, 16, false) | 0.130s | passed |
| testCheckFiles[1]([/tmp/fingerprint8888332551852945861.vcf, /tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint8526523117034821907.vcf], 0, 16, false) | 0.008s | passed |
| testCheckFiles[2]([/tmp/fingerprint11230533161859790849.vcf, /tmp/fingerprint14467713583919176379.vcf, /tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint8526523117034821907.vcf], 1, 16, false) | 0.010s | passed |
| testCheckFiles[3]([/tmp/fingerprint14467713583919176379.vcf, /tmp/fingerprint602062117778355363.vcf, /tmp/fingerprint10019297239983490355.vcf, /tmp/fingerprint602062117778355363.vcf], 0, 9, false) | 0.008s | passed |
| testCheckFiles[4]([/tmp/fingerprint8888332551852945861.vcf, /tmp/fingerprint10019297239983490355.vcf, /tmp/fingerprint602062117778355363.vcf], 0, 16, false) | 0.007s | passed |
| testCheckFiles[5]([/tmp/fingerprint8888332551852945861.vcf, /tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint11230533161859790849.vcf], 1, 16, false) | 0.007s | passed |
| testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, /tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint8526523117034821907.vcf], 0, 36, false) | 0.142s | passed |
| testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam, /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint14467713583919176379.vcf], 1, 16, false) | 0.072s | passed |
| testCheckFiles[8]([/tmp/fingerprint14467713583919176379.vcf, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/fingerprint602062117778355363.vcf], 0, 16, true) | 0.068s | passed |
| testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], 0, 16, true) | 0.117s | passed |
| testCheckPaths[0]([/tmp/fingerprint14467713583919176379.vcf, /tmp/fingerprint602062117778355363.vcf, /tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint8526523117034821907.vcf], /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false) | 0.015s | passed |
| testCheckPaths[1]([/tmp/fingerprint602062117778355363.vcf, /tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint8526523117034821907.vcf], /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false) | 0.011s | passed |
| testCheckPaths[2]([/mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/crosscheck1859143041708754972.fofn], /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false) | 0.012s | passed |
| testCheckSamples[0]([/tmp/fingerprint14467713583919176379.vcf, /tmp/fingerprint602062117778355363.vcf], [/tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint8526523117034821907.vcf], 0, 2, true) | 0.015s | passed |
| testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam, /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam], [/tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint8526523117034821907.vcf], 1, 2, false) | 0.076s | passed |
| testCheckSamples[11]([/tmp/fingerprint14467713583919176379.vcf, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/fingerprint602062117778355363.vcf], 0, 2, true) | 0.071s | passed |
| testCheckSamples[12]([/tmp/fingerprint14467713583919176379.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/fingerprint4717421520942808288.vcf], 1, 2, false) | 0.070s | passed |
| testCheckSamples[13]([/tmp/fingerprint14467713583919176379.vcf, /tmp/fingerprint602062117778355363.vcf], [/tmp/fingerprint10019297239983490355.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam], 1, 2, false) | 0.040s | passed |
| testCheckSamples[14]([/tmp/fingerprint8888332551852945861.vcf], [/tmp/fingerprint10019297239983490355.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam], 1, 2, false) | 0.039s | passed |
| testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], 0, 2, true) | 0.118s | passed |
| testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam], 1, 1, true) | 0.096s | passed |
| testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], 1, 1, true) | 0.095s | passed |
| testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], 1, 2, false) | 0.129s | passed |
| testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], [/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam], 1, 2, false) | 0.121s | passed |
| testCheckSamples[1]([/tmp/fingerprint8888332551852945861.vcf], [/tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint8526523117034821907.vcf], 0, 2, true) | 0.012s | passed |
| testCheckSamples[20]([/tmp/fingerprint14467713583919176379.vcf, /tmp/fingerprint602062117778355363.vcf], [/tmp/fingerprint7827008760857261976.vcf, /tmp/fingerprint8526523117034821907.vcf], 1, 2, false) | 0.016s | passed |
| testCheckSamples[2]([/tmp/fingerprint3579231993969887448.vcf, /tmp/fingerprint15439106532535527298.vcf, /tmp/fingerprint11888033466904643149.vcf], [/tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint8526523117034821907.vcf], 0, 2, true) | 0.013s | passed |
| testCheckSamples[3]([/tmp/fingerprint11230533161859790849.vcf, /tmp/fingerprint14467713583919176379.vcf], [/tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint8526523117034821907.vcf], 1, 2, false) | 0.012s | passed |
| testCheckSamples[4]([/tmp/fingerprint14467713583919176379.vcf, /tmp/fingerprint602062117778355363.vcf], [/tmp/fingerprint10019297239983490355.vcf, /tmp/fingerprint602062117778355363.vcf], 0, 2, true) | 0.011s | passed |
| testCheckSamples[5]([/tmp/fingerprint8888332551852945861.vcf], [/tmp/fingerprint10019297239983490355.vcf, /tmp/fingerprint602062117778355363.vcf], 0, 2, true) | 0.010s | passed |
| testCheckSamples[6]([/tmp/fingerprint8888332551852945861.vcf], [/tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint8526523117034821907.vcf], 0, 2, true) | 0.012s | passed |
| testCheckSamples[7]([/tmp/fingerprint8888332551852945861.vcf], [/tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint11230533161859790849.vcf], 1, 2, false) | 0.011s | passed |
| testCheckSamples[8]([/tmp/fingerprint3579231993969887448.vcf, /tmp/fingerprint15439106532535527298.vcf, /tmp/fingerprint11888033466904643149.vcf], [/tmp/fingerprint10019297239983490355.vcf, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], 0, 2, true) | 0.038s | passed |
| testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], [/tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint8526523117034821907.vcf], 0, 2, true) | 0.121s | passed |
| testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5225960600207950090.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.249s | passed |
| testCramBamComparison[10](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.130s | passed |
| testCramBamComparison[11](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.125s | passed |
| testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5225960600207950090.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.161s | passed |
| testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9659815104115583894.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.173s | passed |
| testCramBamComparison[3](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9659815104115583894.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.152s | passed |
| testCramBamComparison[4](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.154s | passed |
| testCramBamComparison[5](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.138s | passed |
| testCramBamComparison[6](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9659815104115583894.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.129s | passed |
| testCramBamComparison[7](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9659815104115583894.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.119s | passed |
| testCramBamComparison[8](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5225960600207950090.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.123s | passed |
| testCramBamComparison[9](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5225960600207950090.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.116s | passed |
| testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram) | 0.009s | passed |
| testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam) | 0.005s | passed |
| testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram) | 0.004s | passed |
| testCrossCheckIndividuals[0](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, testdata/picard/fingerprint/NA12891_NA12892_different_individuals.txt, 0, 2) | 0.059s | passed |
| testCrossCheckIndividuals[1](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, testdata/picard/fingerprint/NA12891_NA12892_same_individual.txt, 1, 2) | 0.056s | passed |
| testCrossCheckIndividuals[2](/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam, testdata/picard/fingerprint/NA12891_NA12892_different_individuals.txt, 1, 2) | 0.058s | passed |
| testCrossCheckIndividuals[3](/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam, testdata/picard/fingerprint/NA12891_NA12892_same_individual.txt, 0, 2) | 0.059s | passed |
| testCrossCheckLBsWithClustering | 0.141s | passed |
| testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, 0) | 0.060s | passed |
| testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, 0) | 0.059s | passed |
| testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, 0) | 0.063s | passed |
| testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, 0) | 0.062s | passed |
| testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1) | 0.070s | passed |
| testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1) | 0.061s | passed |
| testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1) | 0.061s | passed |
| testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1) | 0.064s | passed |
| testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, false, 0, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.149s | passed |
| testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, false, 0, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.096s | passed |
| testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, false, 0, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.092s | passed |
| testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, true, 0, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.101s | passed |
| testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, true, 0, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.086s | passed |
| testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, true, 1, 2704, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.092s | passed |
| testCrossCheckRGs[15](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, true, 1, 2704, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.090s | passed |
| testCrossCheckRGs[16](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, true, 1, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.111s | passed |
| testCrossCheckRGs[17](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, true, 1, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.092s | passed |
| testCrossCheckRGs[18](/tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, true, 0, 2601, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.099s | passed |
| testCrossCheckRGs[19](/tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, true, 0, 2601, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.081s | passed |
| testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, false, 0, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.099s | passed |
| testCrossCheckRGs[20](/tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, true, 1, 2704, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.095s | passed |
| testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, true, 1, 2704, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.092s | passed |
| testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, true, 1, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.098s | passed |
| testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, true, 1, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.090s | passed |
| testCrossCheckRGs[24](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram, false, 0, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.098s | passed |
| testCrossCheckRGs[25](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram, false, 0, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.089s | passed |
| testCrossCheckRGs[26](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram, false, 0, 2704, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.076s | passed |
| testCrossCheckRGs[27](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram, false, 0, 2704, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.071s | passed |
| testCrossCheckRGs[28](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, false, 0, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.072s | passed |
| testCrossCheckRGs[29](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, false, 0, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.065s | passed |
| testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, false, 0, 2704, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.097s | passed |
| testCrossCheckRGs[30](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, false, 0, 2601, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.074s | passed |
| testCrossCheckRGs[31](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, false, 0, 2601, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.069s | passed |
| testCrossCheckRGs[32](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram, false, 0, 2704, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.070s | passed |
| testCrossCheckRGs[33](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram, false, 0, 2704, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.068s | passed |
| testCrossCheckRGs[34](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, false, 0, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.072s | passed |
| testCrossCheckRGs[35](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, false, 0, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.070s | passed |
| testCrossCheckRGs[36](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram, true, 0, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.071s | passed |
| testCrossCheckRGs[37](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram, true, 0, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.069s | passed |
| testCrossCheckRGs[38](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram, true, 1, 2704, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.069s | passed |
| testCrossCheckRGs[39](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram, true, 1, 2704, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.066s | passed |
| testCrossCheckRGs[3](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, false, 0, 2704, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.097s | passed |
| testCrossCheckRGs[40](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, true, 1, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.078s | passed |
| testCrossCheckRGs[41](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, true, 1, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.069s | passed |
| testCrossCheckRGs[42](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, true, 0, 2601, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.066s | passed |
| testCrossCheckRGs[43](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, true, 0, 2601, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.063s | passed |
| testCrossCheckRGs[44](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram, true, 1, 2704, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.068s | passed |
| testCrossCheckRGs[45](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram, true, 1, 2704, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.062s | passed |
| testCrossCheckRGs[46](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, true, 1, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.077s | passed |
| testCrossCheckRGs[47](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram, true, 1, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.072s | passed |
| testCrossCheckRGs[4](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, false, 0, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.097s | passed |
| testCrossCheckRGs[5](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, false, 0, 2809, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.087s | passed |
| testCrossCheckRGs[6](/tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, false, 0, 2601, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.090s | passed |
| testCrossCheckRGs[7](/tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, false, 0, 2601, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.087s | passed |
| testCrossCheckRGs[8](/tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, false, 0, 2704, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt) | 0.097s | passed |
| testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, false, 0, 2704, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt) | 0.091s | passed |
| testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, 0, 1) | 0.053s | passed |
| testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, 0, 2) | 0.058s | passed |
| testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, 0, 2) | 0.058s | passed |
| testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam, 0, 1) | 0.062s | passed |
| testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam, 1, 2) | 0.064s | passed |
| testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam, 0, 1) | 0.064s | passed |
| testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam, 1, 2) | 0.066s | passed |
| testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, 0) | 0.062s | passed |
| testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, 0) | 0.063s | passed |
| testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, 0) | 0.069s | passed |
| testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, 0) | 0.062s | passed |
| testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam, 1) | 0.065s | passed |
| testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam, 1) | 0.064s | passed |
| testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam, 1) | 0.066s | passed |
| testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam, 1) | 0.069s | passed |
| testExplicitIndexPaths[0]([testdata/picard/fingerprint/index_test/files/NA12891.vcf, testdata/picard/fingerprint/index_test/files/NA12892.vcf.gz, testdata/picard/fingerprint/index_test/files/NA12891.g.vcf, testdata/picard/fingerprint/index_test/files/NA12892.g.vcf], [testdata/picard/fingerprint/index_test/indices/NA12891.vcf.idx, testdata/picard/fingerprint/index_test/indices/NA12892.vcf.gz.tbi, testdata/picard/fingerprint/index_test/indices/NA12891.g.vcf.idx, testdata/picard/fingerprint/index_test/indices/NA12892.g.vcf.idx], 0, 16, false) | 0.025s | passed |
| testExplicitIndexPaths[1]([testdata/picard/fingerprint/index_test/files/NA12891andNA12892.vcf, testdata/picard/fingerprint/index_test/files/NA12891.fp.vcf, testdata/picard/fingerprint/index_test/files/NA12892.vcf.gz], [testdata/picard/fingerprint/index_test/indices/NA12891andNA12892.vcf.idx, testdata/picard/fingerprint/index_test/indices/NA12891.fp.vcf.idx, testdata/picard/fingerprint/index_test/indices/NA12892.vcf.gz.tbi], 0, 16, false) | 0.011s | passed |
| testExplicitIndexPaths[2]([testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r1.bam, testdata/picard/fingerprint/index_test/files/NA12892.over.fingerprints.r1.bam, testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r2.bam, testdata/picard/fingerprint/index_test/files/NA12892.over.fingerprints.r2.bam, testdata/picard/fingerprint/index_test/files/NA12891.g.vcf, testdata/picard/fingerprint/index_test/files/NA12892.g.vcf], [testdata/picard/fingerprint/index_test/indices/NA12891.over.fingerprints.r1.bam.bai, testdata/picard/fingerprint/index_test/indices/NA12892.over.fingerprints.r1.bam.bai, testdata/picard/fingerprint/index_test/indices/NA12891.over.fingerprints.r2.bam.bai, testdata/picard/fingerprint/index_test/indices/NA12892.over.fingerprints.r2.bam.bai, testdata/picard/fingerprint/index_test/indices/NA12891.g.vcf.idx, testdata/picard/fingerprint/index_test/indices/NA12892.g.vcf.idx], 0, 36, false) | 0.120s | passed |
| testExplicitIndexPaths[3]([testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r1.bam, testdata/picard/fingerprint/index_test/files/NA12892.over.fingerprints.r1.bam, testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r2.bam, testdata/picard/fingerprint/index_test/files/NA12892.over.fingerprints.r2.bam], [testdata/picard/fingerprint/index_test/indices/NA12891.over.fingerprints.r1.bam.bai, testdata/picard/fingerprint/index_test/indices/NA12892.over.fingerprints.r1.bam.bai, testdata/picard/fingerprint/index_test/indices/NA12891.over.fingerprints.r2.bam.bai, testdata/picard/fingerprint/index_test/indices/NA12892.over.fingerprints.r2.bam.bai], 0, 16, true) | 0.110s | passed |
| testMissingIndexForced[0]([testdata/picard/fingerprint/index_test/files/NA12891.vcf, testdata/picard/fingerprint/index_test/files/NA12891.fp.vcf], [testdata/picard/fingerprint/index_test/indices/NA12891.vcf.idx]) | 0.010s | passed |
| testMissingIndexForced[1]([testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r1.bam, testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r2.bam], []) | 0.009s | passed |
| testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint14467713583919176379.vcf], [/tmp/fingerprint8888332551852945861.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true) | 0.019s | passed |
| testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], 1, 1, CHECK_SAME_SAMPLE, null, true) | 0.176s | passed |
| testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true) | 0.176s | passed |
| testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam9259756035576409424.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], 1, 2, CHECK_SAME_SAMPLE, null, true) | 0.218s | passed |
| testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true) | 0.209s | passed |
| testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false) | 0.166s | passed |
| testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false) | 0.175s | passed |
| testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam9259756035576409424.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false) | 0.195s | passed |
| testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false) | 0.215s | passed |
| testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam9259756035576409424.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true) | 0.152s | passed |
| testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true) | 0.146s | passed |
| testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true) | 0.015s | passed |
| testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam1104553196726432233.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true) | 0.057s | passed |
| testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true) | 0.056s | passed |
| testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam9259756035576409424.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true) | 0.030s | passed |
| testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true) | 0.028s | passed |
| testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint3521993417099577267.vcf], [/tmp/fingerprint8888332551852945861.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true) | 0.016s | passed |
| testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true) | 0.015s | passed |
| testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint14467713583919176379.vcf], [/tmp/fingerprint8888332551852945861.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false) | 0.017s | passed |
| testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false) | 0.016s | passed |
| testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint3521993417099577267.vcf], [/tmp/fingerprint8888332551852945861.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false) | 0.015s | passed |
| testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false) | 0.015s | passed |
| testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10453431263314259543.vcf], [/tmp/fingerprint8888332551852945861.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true) | 0.016s | passed |
| testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true) | 0.015s | passed |
| testSecondInputCheckAllWithFileMapping | 0.072s | passed |
| testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false) | 0.084s | passed |
| testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false) | 0.087s | passed |
| testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false) | 0.084s | passed |
| testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint14467713583919176379.vcf, /tmp/fingerprint602062117778355363.vcf], [/tmp/fingerprint8526523117034821907.vcf], null, null, 0, 2, 1, false) | 0.009s | passed |
| testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint14467713583919176379.vcf, /tmp/fingerprint602062117778355363.vcf], [/tmp/fingerprint8526523117034821907.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false) | 0.009s | passed |
| testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint602062117778355363.vcf], [/tmp/fingerprint8526523117034821907.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false) | 0.008s | passed |
| testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false) | 0.064s | passed |
| testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint8888332551852945861.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false) | 0.037s | passed |
| testSecondInputCheckAll[0]([/tmp/fingerprint14467713583919176379.vcf, /tmp/fingerprint602062117778355363.vcf], [/tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint8526523117034821907.vcf], 0, 2, 2, true) | 0.013s | passed |
| testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam, /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam], [/tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint8526523117034821907.vcf], 1, 2, 2, false) | 0.062s | passed |
| testSecondInputCheckAll[11]([/tmp/fingerprint14467713583919176379.vcf, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/fingerprint602062117778355363.vcf], 0, 2, 2, true) | 0.059s | passed |
| testSecondInputCheckAll[12]([/tmp/fingerprint14467713583919176379.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/fingerprint4717421520942808288.vcf], 1, 2, 2, false) | 0.062s | passed |
| testSecondInputCheckAll[13]([/tmp/fingerprint14467713583919176379.vcf, /tmp/fingerprint602062117778355363.vcf], [/tmp/fingerprint10019297239983490355.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam], 1, 2, 2, false) | 0.038s | passed |
| testSecondInputCheckAll[14]([/tmp/fingerprint8888332551852945861.vcf], [/tmp/fingerprint10019297239983490355.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam], 1, 2, 2, false) | 0.039s | passed |
| testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], 0, 2, 2, true) | 0.106s | passed |
| testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam], 0, 2, 1, true) | 0.088s | passed |
| testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], 0, 1, 2, true) | 0.082s | passed |
| testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], 1, 2, 2, false) | 0.118s | passed |
| testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], [/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam], 1, 2, 2, false) | 0.125s | passed |
| testSecondInputCheckAll[1]([/tmp/fingerprint8888332551852945861.vcf], [/tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint8526523117034821907.vcf], 0, 2, 2, true) | 0.008s | passed |
| testSecondInputCheckAll[20]([/tmp/fingerprint14467713583919176379.vcf, /tmp/fingerprint602062117778355363.vcf], [/tmp/fingerprint7827008760857261976.vcf, /tmp/fingerprint8526523117034821907.vcf], 1, 2, 2, false) | 0.011s | passed |
| testSecondInputCheckAll[21]([/tmp/fingerprint14467713583919176379.vcf, /tmp/fingerprint602062117778355363.vcf], [/tmp/fingerprint8526523117034821907.vcf], 0, 2, 1, false) | 0.009s | passed |
| testSecondInputCheckAll[22]([/tmp/fingerprint8888332551852945861.vcf], [/tmp/fingerprint8526523117034821907.vcf], 0, 2, 1, false) | 0.009s | passed |
| testSecondInputCheckAll[23]([/tmp/fingerprint3579231993969887448.vcf, /tmp/fingerprint15439106532535527298.vcf, /tmp/fingerprint11888033466904643149.vcf], [/tmp/fingerprint8526523117034821907.vcf], 0, 2, 1, false) | 0.010s | passed |
| testSecondInputCheckAll[24]([/tmp/fingerprint11230533161859790849.vcf, /tmp/fingerprint14467713583919176379.vcf], [/tmp/fingerprint8526523117034821907.vcf], 1, 2, 1, false) | 0.009s | passed |
| testSecondInputCheckAll[25]([/tmp/fingerprint14467713583919176379.vcf, /tmp/fingerprint602062117778355363.vcf], [/tmp/fingerprint602062117778355363.vcf], 0, 2, 1, false) | 0.009s | passed |
| testSecondInputCheckAll[26]([/tmp/fingerprint8888332551852945861.vcf], [/tmp/fingerprint602062117778355363.vcf], 0, 2, 1, false) | 0.008s | passed |
| testSecondInputCheckAll[27]([/tmp/fingerprint8888332551852945861.vcf], [/tmp/fingerprint8526523117034821907.vcf], 0, 2, 1, false) | 0.008s | passed |
| testSecondInputCheckAll[28]([/tmp/fingerprint8888332551852945861.vcf], [/tmp/fingerprint11230533161859790849.vcf], 1, 2, 1, false) | 0.008s | passed |
| testSecondInputCheckAll[29]([/tmp/fingerprint3579231993969887448.vcf, /tmp/fingerprint15439106532535527298.vcf, /tmp/fingerprint11888033466904643149.vcf], [/tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], 0, 2, 1, false) | 0.036s | passed |
| testSecondInputCheckAll[2]([/tmp/fingerprint3579231993969887448.vcf, /tmp/fingerprint15439106532535527298.vcf, /tmp/fingerprint11888033466904643149.vcf], [/tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint8526523117034821907.vcf], 0, 2, 2, true) | 0.010s | passed |
| testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], [/tmp/fingerprint8526523117034821907.vcf], 0, 2, 1, false) | 0.115s | passed |
| testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam, /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam], [/tmp/fingerprint8526523117034821907.vcf], 1, 2, 1, false) | 0.065s | passed |
| testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/fingerprint602062117778355363.vcf], 0, 1, 2, false) | 0.061s | passed |
| testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/fingerprint4717421520942808288.vcf], 1, 1, 2, false) | 0.063s | passed |
| testSecondInputCheckAll[34]([/tmp/fingerprint602062117778355363.vcf], [/tmp/fingerprint10019297239983490355.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam], 1, 1, 2, false) | 0.035s | passed |
| testSecondInputCheckAll[35]([/tmp/fingerprint8888332551852945861.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam], 1, 2, 1, false) | 0.035s | passed |
| testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], 0, 1, 2, false) | 0.088s | passed |
| testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam], 0, 1, 1, false) | 0.057s | passed |
| testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam], [/tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], 0, 1, 1, false) | 0.056s | passed |
| testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam], [/tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], 1, 1, 2, false) | 0.085s | passed |
| testSecondInputCheckAll[3]([/tmp/fingerprint11230533161859790849.vcf, /tmp/fingerprint14467713583919176379.vcf], [/tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint8526523117034821907.vcf], 1, 2, 2, false) | 0.009s | passed |
| testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], [/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam], 1, 1, 2, false) | 0.084s | passed |
| testSecondInputCheckAll[41]([/tmp/fingerprint602062117778355363.vcf], [/tmp/fingerprint7827008760857261976.vcf, /tmp/fingerprint8526523117034821907.vcf], 0, 1, 2, false) | 0.010s | passed |
| testSecondInputCheckAll[4]([/tmp/fingerprint14467713583919176379.vcf, /tmp/fingerprint602062117778355363.vcf], [/tmp/fingerprint10019297239983490355.vcf, /tmp/fingerprint602062117778355363.vcf], 0, 2, 2, true) | 0.008s | passed |
| testSecondInputCheckAll[5]([/tmp/fingerprint8888332551852945861.vcf], [/tmp/fingerprint10019297239983490355.vcf, /tmp/fingerprint602062117778355363.vcf], 0, 2, 2, true) | 0.008s | passed |
| testSecondInputCheckAll[6]([/tmp/fingerprint8888332551852945861.vcf], [/tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint8526523117034821907.vcf], 0, 2, 2, true) | 0.008s | passed |
| testSecondInputCheckAll[7]([/tmp/fingerprint8888332551852945861.vcf], [/tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint11230533161859790849.vcf], 1, 2, 2, false) | 0.009s | passed |
| testSecondInputCheckAll[8]([/tmp/fingerprint3579231993969887448.vcf, /tmp/fingerprint15439106532535527298.vcf, /tmp/fingerprint11888033466904643149.vcf], [/tmp/fingerprint10019297239983490355.vcf, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam], 0, 2, 2, true) | 0.038s | passed |
| testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam, /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam, /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam, /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam], [/tmp/fingerprint6120156480145075008.vcf, /tmp/fingerprint8526523117034821907.vcf], 0, 2, 2, true) | 0.110s | passed |
Standard error
[Thu Apr 24 13:00:15 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --INPUT_SAMPLE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_to_NA12892.txt --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting17054039798411023353test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:15 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:15 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:15 FingerprintChecker Processed files. 2 fingerprints found in map.
[Thu Apr 24 13:00:15 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:15 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --INPUT_SAMPLE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892_to_NA12891.txt --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting7686005268567453620test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:15 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:15 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:15 FingerprintChecker Processed files. 2 fingerprints found in map.
[Thu Apr 24 13:00:15 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --INPUT_SAMPLE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/too_many_fields.txt --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting9058864019935885485test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 2 fingerprints found in map.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --INPUT_SAMPLE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/too_few_fields.txt --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting6377516203923983625test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 2 fingerprints found in map.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --INPUT_SAMPLE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/DuplicateKey.txt --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting16283125461862849576test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 2 fingerprints found in map.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --SECOND_INPUT_SAMPLE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/too_many_fields.txt --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting13832775830237159052test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 1 fingerprints found in map.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --SECOND_INPUT_SAMPLE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/too_few_fields.txt --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting17943002384292132609test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 1 fingerprints found in map.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --SECOND_INPUT_SAMPLE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/DuplicateKey.txt --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting11023420427780399207test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 1 fingerprints found in map.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --INPUT /tmp/fingerprint6120156480145075008.vcf --INPUT /tmp/fingerprint8526523117034821907.vcf --OUTPUT /tmp/Fingerprinting13245073291090095377test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 4 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 4 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Cross-checking all FILE against each other
INFO 2025-04-24 13:00:16 CrosscheckFingerprints All FILEs are related as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --INPUT /tmp/fingerprint6120156480145075008.vcf --INPUT /tmp/fingerprint8526523117034821907.vcf --OUTPUT /tmp/Fingerprinting10349906319214428698test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 3 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 4 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Cross-checking all FILE against each other
INFO 2025-04-24 13:00:16 CrosscheckFingerprints All FILEs are related as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint11230533161859790849.vcf --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint6120156480145075008.vcf --INPUT /tmp/fingerprint8526523117034821907.vcf --OUTPUT /tmp/Fingerprinting14791621947410445753test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 4 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 4 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Cross-checking all FILE against each other
WARNING 2025-04-24 13:00:16 CrosscheckFingerprints 6 FILEs did not relate as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --INPUT /tmp/fingerprint10019297239983490355.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --OUTPUT /tmp/Fingerprinting9550324280618979429test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 4 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 3 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Cross-checking all FILE against each other
INFO 2025-04-24 13:00:16 CrosscheckFingerprints All FILEs are related as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --INPUT /tmp/fingerprint10019297239983490355.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --OUTPUT /tmp/Fingerprinting5803780288730255315test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 3 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 4 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Cross-checking all FILE against each other
INFO 2025-04-24 13:00:16 CrosscheckFingerprints All FILEs are related as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --INPUT /tmp/fingerprint6120156480145075008.vcf --INPUT /tmp/fingerprint11230533161859790849.vcf --OUTPUT /tmp/Fingerprinting1800591363952993064test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 3 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 4 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Cross-checking all FILE against each other
WARNING 2025-04-24 13:00:16 CrosscheckFingerprints 6 FILEs did not relate as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --INPUT /tmp/fingerprint6120156480145075008.vcf --INPUT /tmp/fingerprint8526523117034821907.vcf --OUTPUT /tmp/Fingerprinting8311077329636607435test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 6 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 106 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Cross-checking all FILE against each other
INFO 2025-04-24 13:00:16 CrosscheckFingerprints All FILEs are related as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/fingerprint6120156480145075008.vcf --INPUT /tmp/fingerprint14467713583919176379.vcf --OUTPUT /tmp/Fingerprinting14569253257495911906test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 4 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 56 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Cross-checking all FILE against each other
WARNING 2025-04-24 13:00:16 CrosscheckFingerprints 6 FILEs did not relate as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --INPUT /tmp/fingerprint602062117778355363.vcf --OUTPUT /tmp/Fingerprinting15570619181021394872test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 4 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Cross-checking all FILE against each other
INFO 2025-04-24 13:00:16 CrosscheckFingerprints All FILEs are related as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --OUTPUT /tmp/Fingerprinting3812292603618245978test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 4 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 104 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Cross-checking all FILE against each other
INFO 2025-04-24 13:00:16 CrosscheckFingerprints All FILEs are related as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --OUTPUT /tmp/Fingerprinting9498958329245120176test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 3 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 78 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Cross-checking all FILE against each other
INFO 2025-04-24 13:00:16 CrosscheckFingerprints All FILEs are related as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --OUTPUT /tmp/Fingerprinting1380403962985740550test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 4 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 106 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Cross-checking all FILE against each other
WARNING 2025-04-24 13:00:16 CrosscheckFingerprints 6 FILEs did not relate as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --INPUT /tmp/fingerprint6120156480145075008.vcf --INPUT /tmp/fingerprint8526523117034821907.vcf --OUTPUT /tmp/Fingerprinting6079008625414614625test.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 4 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 4 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Cross-checking all FILE against each other
INFO 2025-04-24 13:00:16 CrosscheckFingerprints All FILEs are related as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint602062117778355363.vcf --INPUT /tmp/fingerprint6120156480145075008.vcf --INPUT /tmp/fingerprint8526523117034821907.vcf --OUTPUT /tmp/Fingerprinting8532259821412847204test.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 3 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 3 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Cross-checking all FILE against each other
INFO 2025-04-24 13:00:16 CrosscheckFingerprints All FILEs are related as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/crosscheck1859143041708754972.fofn --OUTPUT /tmp/Fingerprinting16984753517993084712test.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 3 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 3 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Cross-checking all FILE against each other
INFO 2025-04-24 13:00:16 CrosscheckFingerprints All FILEs are related as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --SECOND_INPUT /tmp/fingerprint6120156480145075008.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --OUTPUT /tmp/Fingerprinting2365832675588839647test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --SECOND_INPUT /tmp/fingerprint6120156480145075008.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --OUTPUT /tmp/Fingerprinting16929004065368447560test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint3579231993969887448.vcf --INPUT /tmp/fingerprint15439106532535527298.vcf --INPUT /tmp/fingerprint11888033466904643149.vcf --SECOND_INPUT /tmp/fingerprint6120156480145075008.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --OUTPUT /tmp/Fingerprinting16071494764456485163test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 3 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 6 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint11230533161859790849.vcf --INPUT /tmp/fingerprint14467713583919176379.vcf --SECOND_INPUT /tmp/fingerprint6120156480145075008.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --OUTPUT /tmp/Fingerprinting7820242546584230871test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:16 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --SECOND_INPUT /tmp/fingerprint10019297239983490355.vcf --SECOND_INPUT /tmp/fingerprint602062117778355363.vcf --OUTPUT /tmp/Fingerprinting13512251305172595678test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --SECOND_INPUT /tmp/fingerprint10019297239983490355.vcf --SECOND_INPUT /tmp/fingerprint602062117778355363.vcf --OUTPUT /tmp/Fingerprinting6358104179494762868test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --SECOND_INPUT /tmp/fingerprint6120156480145075008.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --OUTPUT /tmp/Fingerprinting15613496622562231879test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --SECOND_INPUT /tmp/fingerprint6120156480145075008.vcf --SECOND_INPUT /tmp/fingerprint11230533161859790849.vcf --OUTPUT /tmp/Fingerprinting15996428820710621738test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:16 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint3579231993969887448.vcf --INPUT /tmp/fingerprint15439106532535527298.vcf --INPUT /tmp/fingerprint11888033466904643149.vcf --SECOND_INPUT /tmp/fingerprint10019297239983490355.vcf --SECOND_INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --OUTPUT /tmp/Fingerprinting12416120620363400810test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 3 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 6 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Processed files. 26 fingerprints found in map.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:16 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:16 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --SECOND_INPUT /tmp/fingerprint6120156480145075008.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --OUTPUT /tmp/Fingerprinting11641821575178270886test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:16 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:16 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
INFO 2025-04-24 13:00:16 CrosscheckFingerprints Fingerprinting 4 INPUT files.
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:16 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 104 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:17 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:17 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --SECOND_INPUT /tmp/fingerprint6120156480145075008.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --OUTPUT /tmp/Fingerprinting4305165301046520433test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:17 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:17 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 54 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:17 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:17 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:17 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/fingerprint602062117778355363.vcf --OUTPUT /tmp/Fingerprinting6889892122132324569test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:17 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:17 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 26 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:17 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:17 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/fingerprint4717421520942808288.vcf --OUTPUT /tmp/Fingerprinting15237973861778994867test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:17 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:17 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 28 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:17 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:17 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:17 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --SECOND_INPUT /tmp/fingerprint10019297239983490355.vcf --SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --OUTPUT /tmp/Fingerprinting17148107912434536109test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:17 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:17 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 28 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:17 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:17 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:17 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --SECOND_INPUT /tmp/fingerprint10019297239983490355.vcf --SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --OUTPUT /tmp/Fingerprinting3120833763421589788test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:17 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:17 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 28 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:17 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:17 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:17 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --OUTPUT /tmp/Fingerprinting16074318584824403502test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:17 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:17 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:17 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:17 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --OUTPUT /tmp/Fingerprinting8752535690225788709test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:17 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:17 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 26 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
ERROR 2025-04-24 13:00:17 CrosscheckFingerprints sample NA12892 is missing from RIGHT group
WARNING 2025-04-24 13:00:17 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:17 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:17 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --OUTPUT /tmp/Fingerprinting7421375449977966534test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:17 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:17 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
ERROR 2025-04-24 13:00:17 CrosscheckFingerprints sample NA12892 is missing from LEFT group
WARNING 2025-04-24 13:00:17 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:17 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:17 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --OUTPUT /tmp/Fingerprinting10810338735860487643test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:17 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:17 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 54 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:17 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:17 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:17 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --OUTPUT /tmp/Fingerprinting8122959456757510014test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:17 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:17 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 54 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:17 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:17 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:17 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --SECOND_INPUT /tmp/fingerprint7827008760857261976.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --OUTPUT /tmp/Fingerprinting12003888701787196062test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:17 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:17 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:17 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:17 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:17 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5225960600207950090.bam --OUTPUT /tmp/Fingerprinting.bam.comparison3556519490605411003crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:17 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5225960600207950090.bam)
INFO 2025-04-24 13:00:17 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:17 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:18 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:18 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:18 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram --OUTPUT /tmp/Fingerprinting.cram.comparison1395604855246102170crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:18 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram)
INFO 2025-04-24 13:00:18 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:18 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:18 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:18 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5225960600207950090.bam --OUTPUT /tmp/Fingerprinting.bam.comparison17238757584987889364crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:18 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam)
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5225960600207950090.bam)
INFO 2025-04-24 13:00:18 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:18 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:18 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:18 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram --OUTPUT /tmp/Fingerprinting.cram.comparison138010747860840817crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:18 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram)
INFO 2025-04-24 13:00:18 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:18 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:18 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:18 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9659815104115583894.bam --OUTPUT /tmp/Fingerprinting.bam.comparison6262727322633853617crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:18 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam)
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9659815104115583894.bam)
INFO 2025-04-24 13:00:18 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:18 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:18 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:18 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram --OUTPUT /tmp/Fingerprinting.cram.comparison15545902608443105167crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:18 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram)
INFO 2025-04-24 13:00:18 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:18 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:18 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:18 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9659815104115583894.bam --OUTPUT /tmp/Fingerprinting.bam.comparison10038239365282937499crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:18 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam)
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9659815104115583894.bam)
INFO 2025-04-24 13:00:18 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:18 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:18 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:18 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram --OUTPUT /tmp/Fingerprinting.cram.comparison5151574163082689877crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:18 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram)
INFO 2025-04-24 13:00:18 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:18 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:18 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:18 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam --OUTPUT /tmp/Fingerprinting.bam.comparison578813215190392395crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:18 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam)
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam)
INFO 2025-04-24 13:00:18 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:18 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:18 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:18 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --OUTPUT /tmp/Fingerprinting.cram.comparison17017291994185288815crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:18 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:18 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:18 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:18 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:18 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam --OUTPUT /tmp/Fingerprinting.bam.comparison10308781982819511226crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:18 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam)
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam)
INFO 2025-04-24 13:00:18 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:18 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:18 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:18 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --OUTPUT /tmp/Fingerprinting.cram.comparison11980286681482576366crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:18 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:18 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:18 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:18 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:18 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9659815104115583894.bam --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam --OUTPUT /tmp/Fingerprinting.bam.comparison9606810756343820998crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:18 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9659815104115583894.bam)
INFO 2025-04-24 13:00:18 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam)
INFO 2025-04-24 13:00:18 FingerprintChecker Processed files. 51 fingerprints found in map.
INFO 2025-04-24 13:00:18 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:18 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:18 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:19 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --OUTPUT /tmp/Fingerprinting.cram.comparison772529212712504117crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:19 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram)
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:19 FingerprintChecker Processed files. 51 fingerprints found in map.
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:19 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:19 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:19 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9659815104115583894.bam --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam --OUTPUT /tmp/Fingerprinting.bam.comparison2248766548556883970crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:19 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9659815104115583894.bam)
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam)
INFO 2025-04-24 13:00:19 FingerprintChecker Processed files. 51 fingerprints found in map.
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:19 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:19 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:19 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --OUTPUT /tmp/Fingerprinting.cram.comparison15031296046064966897crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:19 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram)
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:19 FingerprintChecker Processed files. 51 fingerprints found in map.
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:19 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:19 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:19 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5225960600207950090.bam --OUTPUT /tmp/Fingerprinting.bam.comparison1104122733549087926crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:19 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam)
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5225960600207950090.bam)
INFO 2025-04-24 13:00:19 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:19 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:19 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:19 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram --OUTPUT /tmp/Fingerprinting.cram.comparison3642328479491439570crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:19 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram)
INFO 2025-04-24 13:00:19 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:19 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:19 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:19 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5225960600207950090.bam --OUTPUT /tmp/Fingerprinting.bam.comparison6368048960711080013crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:19 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam)
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5225960600207950090.bam)
INFO 2025-04-24 13:00:19 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:19 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:19 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:19 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram --OUTPUT /tmp/Fingerprinting.cram.comparison4949319043897478006crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:19 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram)
INFO 2025-04-24 13:00:19 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:19 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:19 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:19 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam --OUTPUT /tmp/Fingerprinting.bam.comparison2435188155645763880crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:19 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam)
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam)
INFO 2025-04-24 13:00:19 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:19 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:19 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:19 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --OUTPUT /tmp/Fingerprinting.cram.comparison5031862929877181268crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:19 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:19 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:19 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:19 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:19 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam --OUTPUT /tmp/Fingerprinting.bam.comparison3111350405464892768crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:19 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam14825713249556579356.bam)
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13226403108751280613.bam)
INFO 2025-04-24 13:00:19 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:19 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:19 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:19 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --OUTPUT /tmp/Fingerprinting.cram.comparison2536234484576551616crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:19 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:19 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:19 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:19 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
USAGE: CrosscheckFingerprints [arguments]
Checks the odds that all data in the set of input files come from the same individual. Can be used to cross-check
readgroups, libraries, samples, or files. Acceptable inputs include BAM/SAM/CRAM and VCF/GVCF files. Output delivers LOD
scores in the form of a CrosscheckMetric file.
<h3>Summary</h3>
CrosscheckFingerprints rapidly checks the odds that all of the genetic data within a set of files come from the same
individual. This is accomplished by selectively sampling from the input files, and determining whether the genotypes of
the specified Groups match to each other. (Groups are defined by the input and the argument CROSSCHECK_BY; they can be
READ_GROUP, LIBRARY, SAMPLE, or FILE.)<br /><br /> Output is generated in the form of a “molten” (one row per
comparison) CrosscheckMetric file that includes the Logarithm of the Odds (LOD) score, as well as the tumor-aware LOD
score. Tumor-aware LOD scores can be used to assess genotypic identity in the presence of a severe Loss of
Heterozygosity (LOH) with high purity—this could otherwise lead to a failure of the tool to identify samples are from
the same individual. Output is also available as a matrix, to facilitate visual inspection of crosscheck results.<br
/><br /> Metric files can contain many rows of output. We therefore recommend following up CrosscheckFingerprints with a
step using [ClusterCrosscheckMetrics
(Picard)](https://gatk.broadinstitute.org/hc/en-us/articles/360045798972--Tool-Documentation-Index); this tool will
cluster groups together that pass a designated LOD threshold, ensuring that groups within the cluster are related to
each other. <br /><br /> There may be cases where several groups out of a collection of possible groups must be
identified---for example, to link a BAM to its correct sample in a multi-sample VCF. In this case, it would not be
necessary to cross-check the various samples in the VCF against each other, but only to check the identity of the BAM
against the various samples in the VCF. For this application, the SECOND_INPUT argument is provided. With SECOND_INPUT,
CrosscheckFingerprints can do the following: <br /><br /> <ul><li> Independently aggregate data for the input files in
INPUT and SECOND_INPUT. </li><li> Aggregate data at the SAMPLE level. </li><li> Compare samples from INPUT to the same
sample in SECOND_INPUT. </li><li> Disables MATRIX_OUTPUT. </li></ul><br /><br />In some cases, the groups collected may
not have any observations (‘reads’ for BAM files, or ‘calls’ for VCF files) at fingerprinting sites. Alternatively, a
sample in INPUT may be missing from SECOND_INPUT. These cases are handled as follows: <br /><br /> <ul><li> If running
in CHECK_SAME_SAMPLES mode with the INPUT and SECOND_INPUT sets of input files: when either set of inputs (1) includes a
sample not found in the other, or (2) contains a sample with no observations at any fingerprinting sites, then an error
will be logged and the tool will return EXIT_CODE_WHEN_MISMATCH. </li><li> If running in any other running mode: when a
group which is being crosschecked does not have any observations at fingerprinting sites, a warning will be logged.
</li></ul><br /><br />Note that, as long as there is at least one comparison in which both files have observations at
fingerprinting sites, the tool will return a ‘zero’. However, an error will be logged and the tool will return
EXIT_CODE_WHEN_NO_VALID_CHECKS if all comparisons have at least one side without observations at a fingerprinting site
(ie. all LOD scores are zero). <br /><br /> <hr/><h3>Examples</h3><h4>Check that all the readgroups from a sample match
each other:</h4><pre> java -jar picard.jar CrosscheckFingerprints \
INPUT=sample.with.many.readgroups.bam \
HAPLOTYPE_MAP=fingerprinting_haplotype_database.txt \
LOD_THRESHOLD=-5 \
OUTPUT=sample.crosscheck_metrics </pre>
<h4>Check that all the readgroups match as expected when providing reads from two samples from the same individual:</h4>
<pre> java -jar picard.jar CrosscheckFingerprints \
INPUT=sample.one.with.many.readgroups.bam \
INPUT=sample.two.with.many.readgroups.bam \
HAPLOTYPE_MAP=fingerprinting_haplotype_database.txt \
LOD_THRESHOLD=-5 \
EXPECT_ALL_GROUPS_TO_MATCH=true \
OUTPUT=sample.crosscheck_metrics </pre><br /><br /><h4>Detailed Explanation</h4>
This tool calculates the LOD score for identity check between "groups" of data in the INPUT files as defined by the
CROSSCHECK_BY argument. A positive value indicates that the data seems to have come from the same individual or, in
other words the identity checks out. The scale is logarithmic (base 10), so a LOD of 6 indicates that it is 1,000,000
more likely that the data matches the genotypes than not. A negative value indicates that the data do not match. A score
that is near zero is inconclusive and can result from low coverage or non-informative genotypes. <br /><br />Each group
is assigned a sample identifier (for SAM this is taken from the SM tag in the appropriate readgroup header line, for VCF
this is taken from the column label in the file-header. After combining all the data from the same group together, an
all-against-all comparison is performed. Results are categorized as one of EXPECTED_MATCH, EXPECTED_MISMATCH,
UNEXPECTED_MATCH, UNEXPECTED_MISMATCH, or AMBIGUOUS depending on the LOD score and on whether the sample identifiers of
the groups agree: LOD scores that are less than LOD_THRESHOLD are considered mismatches, and those greater than
-LOD_THRESHOLD are matches (between is ambiguous). If the sample identifiers are equal, the groups are expected to
match. They are expected to mismatch otherwise. <br /><br />The identity check makes use of haplotype blocks defined in
the HAPLOTYPE_MAP file to enable it to have higher statistical power for detecting identity or swap by aggregating data
from several SNPs in the haplotype block. This enables an identity check of samples with very low coverage (e.g. ~1x
mean coverage).<br /><br />When provided a VCF, the identity check looks at the PL, GL and GT fields (in that order) and
uses the first one that it finds.
Version:null
Required Arguments:
--HAPLOTYPE_MAP,-H <File> The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for
fingerprinting. See
https://gatk.broadinstitute.org/hc/en-us/articles/360035531672-Haplotype-map-format for
details. Required.
--INPUT,-I <String> One or more input files (or lists of files) with which to compare fingerprints. This
argument must be specified at least once. Required.
Optional Arguments:
--ALLOW_DUPLICATE_READS <Boolean>
Allow the use of duplicate reads in performing the comparison. Can be useful when
duplicate marking has been overly aggressive and coverage is low. Default value: false.
Possible values: {true, false}
--arguments_file <File> read one or more arguments files and add them to the command line This argument may be
specified 0 or more times. Default value: null.
--CALCULATE_TUMOR_AWARE_RESULTS <Boolean>
Specifies whether the Tumor-aware result should be calculated. These are time consuming
and can roughly double the runtime of the tool. When crosschecking many groups not
calculating the tumor-aware results can result in a significant speedup. Default value:
true. Possible values: {true, false}
--COMPRESSION_LEVEL <Integer> Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5.
--CREATE_INDEX <Boolean> Whether to create an index when writing VCF or coordinate sorted BAM output. Default
value: false. Possible values: {true, false}
--CREATE_MD5_FILE <Boolean> Whether to create an MD5 digest for any BAM or FASTQ files created. Default value:
false. Possible values: {true, false}
--CROSSCHECK_BY <DataType> Specifies which data-type should be used as the basic comparison unit. Fingerprints from
readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared.
Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP.
Possible values: {FILE, SAMPLE, LIBRARY, READGROUP}
--CROSSCHECK_MODE <CrosscheckMode>
An argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur.
Default value: CHECK_SAME_SAMPLE. CHECK_SAME_SAMPLE (In this mode, each sample in INPUT
will only be checked against a single corresponding sample in SECOND_INPUT. If a
corresponding sample cannot be found, the program will proceed, but report the missing
samples and return the value specified in EXIT_CODE_WHEN_MISMATCH. The corresponding
samples are those that equal each other, after possible renaming via INPUT_SAMPLE_MAP and
SECOND_INPUT_SAMPLE_MAP. In this mode CROSSCHECK_BY must be SAMPLE.)
CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the
samples in SECOND_INPUT.)
--EXIT_CODE_WHEN_MISMATCH <Integer>
When one or more mismatches between groups is detected, exit with this value instead of 0.
Default value: 1.
--EXIT_CODE_WHEN_NO_VALID_CHECKS <Integer>
When all LOD scores are zero, exit with this value. Default value: 1.
--EXPECT_ALL_GROUPS_TO_MATCH <Boolean>
Expect all groups' fingerprints to match, irrespective of their sample names. By default
(with this value set to false), groups (readgroups, libraries, files, or samples) with
different sample names are expected to mismatch, and those with the same sample name are
expected to match. Default value: false. Possible values: {true, false}
--GENOTYPING_ERROR_RATE <Double>
This argument is DEPRECATED (No longer used in fingerprint checking. Will be removed in a
future release.). Assumed genotyping error rate that provides a floor on the probability
that a genotype comes from the expected sample. Must be greater than zero. Default
value: 0.01.
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--INPUT_INDEX_MAP <File> A tsv with two columns and no header which maps the input files to corresponding indices;
to be used when index files are not located next to input files. First column must match
the list of inputs. Default value: null.
--INPUT_SAMPLE_FILE_MAP <File>A tsv with two columns representing the sample as it should be used for comparisons to
SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in
the second column). Need only to include the samples that change. Values in column 1
should be unique even in union with the remaining unmapped samples. Values in column 2
should be unique in the file. Will error if more than one sample is found in a file
(multi-sample VCF) pointed to in column 2. Should only be used in the presence of
SECOND_INPUT. Default value: null. Cannot be used in conjunction with argument(s)
INPUT_SAMPLE_MAP
--INPUT_SAMPLE_MAP <File> A tsv with two columns representing the sample as it appears in the INPUT data (in column
1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second
column). Need only include the samples that change. Values in column 1 should be unique.
Values in column 2 should be unique even in union with the remaining unmapped samples.
Should only be used with SECOND_INPUT. Default value: null. Cannot be used in
conjunction with argument(s) INPUT_SAMPLE_FILE_MAP
--LOD_THRESHOLD,-LOD <Double> If any two groups (with the same sample name) match with a LOD score lower than the
threshold the tool will exit with a non-zero code to indicate error. Program will also
exit with an error if it finds two groups with different sample name that match with a LOD
score greater than -LOD_THRESHOLD.
LOD score 0 means equal likelihood that the groups match vs. come from different
individuals, negative LOD score -N, mean 10^N time more likely that the groups are from
different individuals, and +N means 10^N times more likely that the groups are from the
same individual. Default value: 0.0.
--LOSS_OF_HET_RATE <Double> The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via
loss of heterozygosity) in the tumor (model assumes independent events, so this needs to
be larger than reality). Default value: 0.5.
--MATRIX_OUTPUT,-MO <File> Optional output file to write matrix of LOD scores to. This is less informative than the
metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of
Heterozygosity). It is however sometimes easier to use visually. Default value: null.
Cannot be used in conjunction with argument(s) SECOND_INPUT (SI)
--MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK <Double>
Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood
difference between the different values for the three possible genotypes). Default value:
3.0.
--MAX_RECORDS_IN_RAM <Integer>When writing files that need to be sorted, this will specify the number of records stored
in RAM before spilling to disk. Increasing this number reduces the number of file handles
needed to sort the file, and increases the amount of RAM needed. Default value: 500000.
--NUM_THREADS <Integer> The number of threads to use to process files and generate fingerprints. Default value:
1.
--OUTPUT,-O <File> Optional output file to write metrics to. Default is to write to stdout. Default value:
null.
--OUTPUT_ERRORS_ONLY <Boolean>If true, then only groups that do not relate to each other as expected will have their
LODs reported. Default value: false. Possible values: {true, false}
--QUIET <Boolean> Whether to suppress job-summary info on System.err. Default value: false. Possible
values: {true, false}
--REFERENCE_SEQUENCE,-R <PicardHtsPath>
Reference sequence file. Default value: null.
--REQUIRE_INDEX_FILES <Boolean>
A boolean value to determine whether input files should only be parsed if index files are
available. Without turning this option on, the tool will need to read through the entirety
of input files without index files either provided via the INPUT_INDEX_MAP or locally
accessible relative to the input, which significantly increases runtime. If set to true
and no index is found for a file, an exception will be thrown. This applies for both the
INPUT and SECOND_INPUT files. Default value: false. Possible values: {true, false}
--SAMPLE_INDIVIDUAL_MAP <File>A tsv with two columns representing the individual with which each sample is associated.
The first column is the sample id, and the second column is the associated individual id.
Values in the first column must be unique. If INPUT_SAMPLE_MAP or SECOND_INPUT_SAMPLE_MAP
is also specified, then the values in the first column of this file should be the sample
aliases specified in the second columns of INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP,
respectively. When this input is specified, expectations for matches will be based on the
equality or inequality of the individual ids associated with two samples, as opposed to
the sample ids themselves. Samples which are not listed in this file will have their
sample id used as their individual id, for the purposes of match expectations. This means
that one sample id could be used as the individual id for another sample, but not included
in the map itself, and these two samples would be considered to have come from the same
individual. Note that use of this parameter only affects labelling of matches and
mismatches as EXPECTED or UNEXPECTED. It has no affect on how data is grouped for
crosschecking. Default value: null.
--SECOND_INPUT,-SI <String> A second set of input files (or lists of files) with which to compare fingerprints. If
this option is provided the tool compares each sample in INPUT with the sample from
SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE
regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in
INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool
will proceed to check the matching samples, but report the missing samples and return a
non-zero error-code. This argument may be specified 0 or more times. Default value: null.
Cannot be used in conjunction with argument(s) MATRIX_OUTPUT (MO)
--SECOND_INPUT_INDEX_MAP <File>
A tsv with two columns and no header which maps the second input files to corresponding
indices; to be used when index files are not located next to second input files. First
column must match the list of second inputs. Default value: null.
--SECOND_INPUT_SAMPLE_MAP <File>
A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in
column 1) and the sample as it should be used for comparisons to INPUT (in the second
column). Note that in case of unrolling files (file-of-filenames) one would need to
reference the final file, i.e. the file that contains the genomic data. Need only include
the samples that change. Values in column 1 should be unique. Values in column 2 should be
unique even in union with the remaining unmapped samples. Should only be used with
SECOND_INPUT. Default value: null.
--TMP_DIR <File> One or more directories with space available to be used by this program for temporary
storage of working files This argument may be specified 0 or more times. Default value:
null.
--USE_JDK_DEFLATER,-use_jdk_deflater <Boolean>
Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default
value: false. Possible values: {true, false}
--USE_JDK_INFLATER,-use_jdk_inflater <Boolean>
Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default
value: false. Possible values: {true, false}
--VALIDATION_STRINGENCY <ValidationStringency>
Validation stringency for all SAM files read by this program. Setting stringency to
SILENT can improve performance when processing a BAM file in which variable-length data
(read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT.
Possible values: {STRICT, LENIENT, SILENT}
--VERBOSITY <LogLevel> Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
INFO, DEBUG}
--version <Boolean> display the version number for this tool Default value: false. Possible values: {true,
false}
Advanced Arguments:
--showHidden <Boolean> display hidden arguments Default value: false. Possible values: {true, false}
REFERENCE must be provided when using CRAM as input.
USAGE: CrosscheckFingerprints [arguments]
Checks the odds that all data in the set of input files come from the same individual. Can be used to cross-check
readgroups, libraries, samples, or files. Acceptable inputs include BAM/SAM/CRAM and VCF/GVCF files. Output delivers LOD
scores in the form of a CrosscheckMetric file.
<h3>Summary</h3>
CrosscheckFingerprints rapidly checks the odds that all of the genetic data within a set of files come from the same
individual. This is accomplished by selectively sampling from the input files, and determining whether the genotypes of
the specified Groups match to each other. (Groups are defined by the input and the argument CROSSCHECK_BY; they can be
READ_GROUP, LIBRARY, SAMPLE, or FILE.)<br /><br /> Output is generated in the form of a “molten” (one row per
comparison) CrosscheckMetric file that includes the Logarithm of the Odds (LOD) score, as well as the tumor-aware LOD
score. Tumor-aware LOD scores can be used to assess genotypic identity in the presence of a severe Loss of
Heterozygosity (LOH) with high purity—this could otherwise lead to a failure of the tool to identify samples are from
the same individual. Output is also available as a matrix, to facilitate visual inspection of crosscheck results.<br
/><br /> Metric files can contain many rows of output. We therefore recommend following up CrosscheckFingerprints with a
step using [ClusterCrosscheckMetrics
(Picard)](https://gatk.broadinstitute.org/hc/en-us/articles/360045798972--Tool-Documentation-Index); this tool will
cluster groups together that pass a designated LOD threshold, ensuring that groups within the cluster are related to
each other. <br /><br /> There may be cases where several groups out of a collection of possible groups must be
identified---for example, to link a BAM to its correct sample in a multi-sample VCF. In this case, it would not be
necessary to cross-check the various samples in the VCF against each other, but only to check the identity of the BAM
against the various samples in the VCF. For this application, the SECOND_INPUT argument is provided. With SECOND_INPUT,
CrosscheckFingerprints can do the following: <br /><br /> <ul><li> Independently aggregate data for the input files in
INPUT and SECOND_INPUT. </li><li> Aggregate data at the SAMPLE level. </li><li> Compare samples from INPUT to the same
sample in SECOND_INPUT. </li><li> Disables MATRIX_OUTPUT. </li></ul><br /><br />In some cases, the groups collected may
not have any observations (‘reads’ for BAM files, or ‘calls’ for VCF files) at fingerprinting sites. Alternatively, a
sample in INPUT may be missing from SECOND_INPUT. These cases are handled as follows: <br /><br /> <ul><li> If running
in CHECK_SAME_SAMPLES mode with the INPUT and SECOND_INPUT sets of input files: when either set of inputs (1) includes a
sample not found in the other, or (2) contains a sample with no observations at any fingerprinting sites, then an error
will be logged and the tool will return EXIT_CODE_WHEN_MISMATCH. </li><li> If running in any other running mode: when a
group which is being crosschecked does not have any observations at fingerprinting sites, a warning will be logged.
</li></ul><br /><br />Note that, as long as there is at least one comparison in which both files have observations at
fingerprinting sites, the tool will return a ‘zero’. However, an error will be logged and the tool will return
EXIT_CODE_WHEN_NO_VALID_CHECKS if all comparisons have at least one side without observations at a fingerprinting site
(ie. all LOD scores are zero). <br /><br /> <hr/><h3>Examples</h3><h4>Check that all the readgroups from a sample match
each other:</h4><pre> java -jar picard.jar CrosscheckFingerprints \
INPUT=sample.with.many.readgroups.bam \
HAPLOTYPE_MAP=fingerprinting_haplotype_database.txt \
LOD_THRESHOLD=-5 \
OUTPUT=sample.crosscheck_metrics </pre>
<h4>Check that all the readgroups match as expected when providing reads from two samples from the same individual:</h4>
<pre> java -jar picard.jar CrosscheckFingerprints \
INPUT=sample.one.with.many.readgroups.bam \
INPUT=sample.two.with.many.readgroups.bam \
HAPLOTYPE_MAP=fingerprinting_haplotype_database.txt \
LOD_THRESHOLD=-5 \
EXPECT_ALL_GROUPS_TO_MATCH=true \
OUTPUT=sample.crosscheck_metrics </pre><br /><br /><h4>Detailed Explanation</h4>
This tool calculates the LOD score for identity check between "groups" of data in the INPUT files as defined by the
CROSSCHECK_BY argument. A positive value indicates that the data seems to have come from the same individual or, in
other words the identity checks out. The scale is logarithmic (base 10), so a LOD of 6 indicates that it is 1,000,000
more likely that the data matches the genotypes than not. A negative value indicates that the data do not match. A score
that is near zero is inconclusive and can result from low coverage or non-informative genotypes. <br /><br />Each group
is assigned a sample identifier (for SAM this is taken from the SM tag in the appropriate readgroup header line, for VCF
this is taken from the column label in the file-header. After combining all the data from the same group together, an
all-against-all comparison is performed. Results are categorized as one of EXPECTED_MATCH, EXPECTED_MISMATCH,
UNEXPECTED_MATCH, UNEXPECTED_MISMATCH, or AMBIGUOUS depending on the LOD score and on whether the sample identifiers of
the groups agree: LOD scores that are less than LOD_THRESHOLD are considered mismatches, and those greater than
-LOD_THRESHOLD are matches (between is ambiguous). If the sample identifiers are equal, the groups are expected to
match. They are expected to mismatch otherwise. <br /><br />The identity check makes use of haplotype blocks defined in
the HAPLOTYPE_MAP file to enable it to have higher statistical power for detecting identity or swap by aggregating data
from several SNPs in the haplotype block. This enables an identity check of samples with very low coverage (e.g. ~1x
mean coverage).<br /><br />When provided a VCF, the identity check looks at the PL, GL and GT fields (in that order) and
uses the first one that it finds.
Version:null
Required Arguments:
--HAPLOTYPE_MAP,-H <File> The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for
fingerprinting. See
https://gatk.broadinstitute.org/hc/en-us/articles/360035531672-Haplotype-map-format for
details. Required.
--INPUT,-I <String> One or more input files (or lists of files) with which to compare fingerprints. This
argument must be specified at least once. Required.
Optional Arguments:
--ALLOW_DUPLICATE_READS <Boolean>
Allow the use of duplicate reads in performing the comparison. Can be useful when
duplicate marking has been overly aggressive and coverage is low. Default value: false.
Possible values: {true, false}
--arguments_file <File> read one or more arguments files and add them to the command line This argument may be
specified 0 or more times. Default value: null.
--CALCULATE_TUMOR_AWARE_RESULTS <Boolean>
Specifies whether the Tumor-aware result should be calculated. These are time consuming
and can roughly double the runtime of the tool. When crosschecking many groups not
calculating the tumor-aware results can result in a significant speedup. Default value:
true. Possible values: {true, false}
--COMPRESSION_LEVEL <Integer> Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5.
--CREATE_INDEX <Boolean> Whether to create an index when writing VCF or coordinate sorted BAM output. Default
value: false. Possible values: {true, false}
--CREATE_MD5_FILE <Boolean> Whether to create an MD5 digest for any BAM or FASTQ files created. Default value:
false. Possible values: {true, false}
--CROSSCHECK_BY <DataType> Specifies which data-type should be used as the basic comparison unit. Fingerprints from
readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared.
Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP.
Possible values: {FILE, SAMPLE, LIBRARY, READGROUP}
--CROSSCHECK_MODE <CrosscheckMode>
An argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur.
Default value: CHECK_SAME_SAMPLE. CHECK_SAME_SAMPLE (In this mode, each sample in INPUT
will only be checked against a single corresponding sample in SECOND_INPUT. If a
corresponding sample cannot be found, the program will proceed, but report the missing
samples and return the value specified in EXIT_CODE_WHEN_MISMATCH. The corresponding
samples are those that equal each other, after possible renaming via INPUT_SAMPLE_MAP and
SECOND_INPUT_SAMPLE_MAP. In this mode CROSSCHECK_BY must be SAMPLE.)
CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the
samples in SECOND_INPUT.)
--EXIT_CODE_WHEN_MISMATCH <Integer>
When one or more mismatches between groups is detected, exit with this value instead of 0.
Default value: 1.
--EXIT_CODE_WHEN_NO_VALID_CHECKS <Integer>
When all LOD scores are zero, exit with this value. Default value: 1.
--EXPECT_ALL_GROUPS_TO_MATCH <Boolean>
Expect all groups' fingerprints to match, irrespective of their sample names. By default
(with this value set to false), groups (readgroups, libraries, files, or samples) with
different sample names are expected to mismatch, and those with the same sample name are
expected to match. Default value: false. Possible values: {true, false}
--GENOTYPING_ERROR_RATE <Double>
This argument is DEPRECATED (No longer used in fingerprint checking. Will be removed in a
future release.). Assumed genotyping error rate that provides a floor on the probability
that a genotype comes from the expected sample. Must be greater than zero. Default
value: 0.01.
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--INPUT_INDEX_MAP <File> A tsv with two columns and no header which maps the input files to corresponding indices;
to be used when index files are not located next to input files. First column must match
the list of inputs. Default value: null.
--INPUT_SAMPLE_FILE_MAP <File>A tsv with two columns representing the sample as it should be used for comparisons to
SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in
the second column). Need only to include the samples that change. Values in column 1
should be unique even in union with the remaining unmapped samples. Values in column 2
should be unique in the file. Will error if more than one sample is found in a file
(multi-sample VCF) pointed to in column 2. Should only be used in the presence of
SECOND_INPUT. Default value: null. Cannot be used in conjunction with argument(s)
INPUT_SAMPLE_MAP
--INPUT_SAMPLE_MAP <File> A tsv with two columns representing the sample as it appears in the INPUT data (in column
1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second
column). Need only include the samples that change. Values in column 1 should be unique.
Values in column 2 should be unique even in union with the remaining unmapped samples.
Should only be used with SECOND_INPUT. Default value: null. Cannot be used in
conjunction with argument(s) INPUT_SAMPLE_FILE_MAP
--LOD_THRESHOLD,-LOD <Double> If any two groups (with the same sample name) match with a LOD score lower than the
threshold the tool will exit with a non-zero code to indicate error. Program will also
exit with an error if it finds two groups with different sample name that match with a LOD
score greater than -LOD_THRESHOLD.
LOD score 0 means equal likelihood that the groups match vs. come from different
individuals, negative LOD score -N, mean 10^N time more likely that the groups are from
different individuals, and +N means 10^N times more likely that the groups are from the
same individual. Default value: 0.0.
--LOSS_OF_HET_RATE <Double> The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via
loss of heterozygosity) in the tumor (model assumes independent events, so this needs to
be larger than reality). Default value: 0.5.
--MATRIX_OUTPUT,-MO <File> Optional output file to write matrix of LOD scores to. This is less informative than the
metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of
Heterozygosity). It is however sometimes easier to use visually. Default value: null.
Cannot be used in conjunction with argument(s) SECOND_INPUT (SI)
--MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK <Double>
Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood
difference between the different values for the three possible genotypes). Default value:
3.0.
--MAX_RECORDS_IN_RAM <Integer>When writing files that need to be sorted, this will specify the number of records stored
in RAM before spilling to disk. Increasing this number reduces the number of file handles
needed to sort the file, and increases the amount of RAM needed. Default value: 500000.
--NUM_THREADS <Integer> The number of threads to use to process files and generate fingerprints. Default value:
1.
--OUTPUT,-O <File> Optional output file to write metrics to. Default is to write to stdout. Default value:
null.
--OUTPUT_ERRORS_ONLY <Boolean>If true, then only groups that do not relate to each other as expected will have their
LODs reported. Default value: false. Possible values: {true, false}
--QUIET <Boolean> Whether to suppress job-summary info on System.err. Default value: false. Possible
values: {true, false}
--REFERENCE_SEQUENCE,-R <PicardHtsPath>
Reference sequence file. Default value: null.
--REQUIRE_INDEX_FILES <Boolean>
A boolean value to determine whether input files should only be parsed if index files are
available. Without turning this option on, the tool will need to read through the entirety
of input files without index files either provided via the INPUT_INDEX_MAP or locally
accessible relative to the input, which significantly increases runtime. If set to true
and no index is found for a file, an exception will be thrown. This applies for both the
INPUT and SECOND_INPUT files. Default value: false. Possible values: {true, false}
--SAMPLE_INDIVIDUAL_MAP <File>A tsv with two columns representing the individual with which each sample is associated.
The first column is the sample id, and the second column is the associated individual id.
Values in the first column must be unique. If INPUT_SAMPLE_MAP or SECOND_INPUT_SAMPLE_MAP
is also specified, then the values in the first column of this file should be the sample
aliases specified in the second columns of INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP,
respectively. When this input is specified, expectations for matches will be based on the
equality or inequality of the individual ids associated with two samples, as opposed to
the sample ids themselves. Samples which are not listed in this file will have their
sample id used as their individual id, for the purposes of match expectations. This means
that one sample id could be used as the individual id for another sample, but not included
in the map itself, and these two samples would be considered to have come from the same
individual. Note that use of this parameter only affects labelling of matches and
mismatches as EXPECTED or UNEXPECTED. It has no affect on how data is grouped for
crosschecking. Default value: null.
--SECOND_INPUT,-SI <String> A second set of input files (or lists of files) with which to compare fingerprints. If
this option is provided the tool compares each sample in INPUT with the sample from
SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE
regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in
INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool
will proceed to check the matching samples, but report the missing samples and return a
non-zero error-code. This argument may be specified 0 or more times. Default value: null.
Cannot be used in conjunction with argument(s) MATRIX_OUTPUT (MO)
--SECOND_INPUT_INDEX_MAP <File>
A tsv with two columns and no header which maps the second input files to corresponding
indices; to be used when index files are not located next to second input files. First
column must match the list of second inputs. Default value: null.
--SECOND_INPUT_SAMPLE_MAP <File>
A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in
column 1) and the sample as it should be used for comparisons to INPUT (in the second
column). Note that in case of unrolling files (file-of-filenames) one would need to
reference the final file, i.e. the file that contains the genomic data. Need only include
the samples that change. Values in column 1 should be unique. Values in column 2 should be
unique even in union with the remaining unmapped samples. Should only be used with
SECOND_INPUT. Default value: null.
--TMP_DIR <File> One or more directories with space available to be used by this program for temporary
storage of working files This argument may be specified 0 or more times. Default value:
null.
--USE_JDK_DEFLATER,-use_jdk_deflater <Boolean>
Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default
value: false. Possible values: {true, false}
--USE_JDK_INFLATER,-use_jdk_inflater <Boolean>
Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default
value: false. Possible values: {true, false}
--VALIDATION_STRINGENCY <ValidationStringency>
Validation stringency for all SAM files read by this program. Setting stringency to
SILENT can improve performance when processing a BAM file in which variable-length data
(read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT.
Possible values: {STRICT, LENIENT, SILENT}
--VERBOSITY <LogLevel> Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
INFO, DEBUG}
--version <Boolean> display the version number for this tool Default value: false. Possible values: {true,
false}
Advanced Arguments:
--showHidden <Boolean> display hidden arguments Default value: false. Possible values: {true, false}
REFERENCE must be provided when using CRAM as input.
USAGE: CrosscheckFingerprints [arguments]
Checks the odds that all data in the set of input files come from the same individual. Can be used to cross-check
readgroups, libraries, samples, or files. Acceptable inputs include BAM/SAM/CRAM and VCF/GVCF files. Output delivers LOD
scores in the form of a CrosscheckMetric file.
<h3>Summary</h3>
CrosscheckFingerprints rapidly checks the odds that all of the genetic data within a set of files come from the same
individual. This is accomplished by selectively sampling from the input files, and determining whether the genotypes of
the specified Groups match to each other. (Groups are defined by the input and the argument CROSSCHECK_BY; they can be
READ_GROUP, LIBRARY, SAMPLE, or FILE.)<br /><br /> Output is generated in the form of a “molten” (one row per
comparison) CrosscheckMetric file that includes the Logarithm of the Odds (LOD) score, as well as the tumor-aware LOD
score. Tumor-aware LOD scores can be used to assess genotypic identity in the presence of a severe Loss of
Heterozygosity (LOH) with high purity—this could otherwise lead to a failure of the tool to identify samples are from
the same individual. Output is also available as a matrix, to facilitate visual inspection of crosscheck results.<br
/><br /> Metric files can contain many rows of output. We therefore recommend following up CrosscheckFingerprints with a
step using [ClusterCrosscheckMetrics
(Picard)](https://gatk.broadinstitute.org/hc/en-us/articles/360045798972--Tool-Documentation-Index); this tool will
cluster groups together that pass a designated LOD threshold, ensuring that groups within the cluster are related to
each other. <br /><br /> There may be cases where several groups out of a collection of possible groups must be
identified---for example, to link a BAM to its correct sample in a multi-sample VCF. In this case, it would not be
necessary to cross-check the various samples in the VCF against each other, but only to check the identity of the BAM
against the various samples in the VCF. For this application, the SECOND_INPUT argument is provided. With SECOND_INPUT,
CrosscheckFingerprints can do the following: <br /><br /> <ul><li> Independently aggregate data for the input files in
INPUT and SECOND_INPUT. </li><li> Aggregate data at the SAMPLE level. </li><li> Compare samples from INPUT to the same
sample in SECOND_INPUT. </li><li> Disables MATRIX_OUTPUT. </li></ul><br /><br />In some cases, the groups collected may
not have any observations (‘reads’ for BAM files, or ‘calls’ for VCF files) at fingerprinting sites. Alternatively, a
sample in INPUT may be missing from SECOND_INPUT. These cases are handled as follows: <br /><br /> <ul><li> If running
in CHECK_SAME_SAMPLES mode with the INPUT and SECOND_INPUT sets of input files: when either set of inputs (1) includes a
sample not found in the other, or (2) contains a sample with no observations at any fingerprinting sites, then an error
will be logged and the tool will return EXIT_CODE_WHEN_MISMATCH. </li><li> If running in any other running mode: when a
group which is being crosschecked does not have any observations at fingerprinting sites, a warning will be logged.
</li></ul><br /><br />Note that, as long as there is at least one comparison in which both files have observations at
fingerprinting sites, the tool will return a ‘zero’. However, an error will be logged and the tool will return
EXIT_CODE_WHEN_NO_VALID_CHECKS if all comparisons have at least one side without observations at a fingerprinting site
(ie. all LOD scores are zero). <br /><br /> <hr/><h3>Examples</h3><h4>Check that all the readgroups from a sample match
each other:</h4><pre> java -jar picard.jar CrosscheckFingerprints \
INPUT=sample.with.many.readgroups.bam \
HAPLOTYPE_MAP=fingerprinting_haplotype_database.txt \
LOD_THRESHOLD=-5 \
OUTPUT=sample.crosscheck_metrics </pre>
<h4>Check that all the readgroups match as expected when providing reads from two samples from the same individual:</h4>
<pre> java -jar picard.jar CrosscheckFingerprints \
INPUT=sample.one.with.many.readgroups.bam \
INPUT=sample.two.with.many.readgroups.bam \
HAPLOTYPE_MAP=fingerprinting_haplotype_database.txt \
LOD_THRESHOLD=-5 \
EXPECT_ALL_GROUPS_TO_MATCH=true \
OUTPUT=sample.crosscheck_metrics </pre><br /><br /><h4>Detailed Explanation</h4>
This tool calculates the LOD score for identity check between "groups" of data in the INPUT files as defined by the
CROSSCHECK_BY argument. A positive value indicates that the data seems to have come from the same individual or, in
other words the identity checks out. The scale is logarithmic (base 10), so a LOD of 6 indicates that it is 1,000,000
more likely that the data matches the genotypes than not. A negative value indicates that the data do not match. A score
that is near zero is inconclusive and can result from low coverage or non-informative genotypes. <br /><br />Each group
is assigned a sample identifier (for SAM this is taken from the SM tag in the appropriate readgroup header line, for VCF
this is taken from the column label in the file-header. After combining all the data from the same group together, an
all-against-all comparison is performed. Results are categorized as one of EXPECTED_MATCH, EXPECTED_MISMATCH,
UNEXPECTED_MATCH, UNEXPECTED_MISMATCH, or AMBIGUOUS depending on the LOD score and on whether the sample identifiers of
the groups agree: LOD scores that are less than LOD_THRESHOLD are considered mismatches, and those greater than
-LOD_THRESHOLD are matches (between is ambiguous). If the sample identifiers are equal, the groups are expected to
match. They are expected to mismatch otherwise. <br /><br />The identity check makes use of haplotype blocks defined in
the HAPLOTYPE_MAP file to enable it to have higher statistical power for detecting identity or swap by aggregating data
from several SNPs in the haplotype block. This enables an identity check of samples with very low coverage (e.g. ~1x
mean coverage).<br /><br />When provided a VCF, the identity check looks at the PL, GL and GT fields (in that order) and
uses the first one that it finds.
Version:null
Required Arguments:
--HAPLOTYPE_MAP,-H <File> The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for
fingerprinting. See
https://gatk.broadinstitute.org/hc/en-us/articles/360035531672-Haplotype-map-format for
details. Required.
--INPUT,-I <String> One or more input files (or lists of files) with which to compare fingerprints. This
argument must be specified at least once. Required.
Optional Arguments:
--ALLOW_DUPLICATE_READS <Boolean>
Allow the use of duplicate reads in performing the comparison. Can be useful when
duplicate marking has been overly aggressive and coverage is low. Default value: false.
Possible values: {true, false}
--arguments_file <File> read one or more arguments files and add them to the command line This argument may be
specified 0 or more times. Default value: null.
--CALCULATE_TUMOR_AWARE_RESULTS <Boolean>
Specifies whether the Tumor-aware result should be calculated. These are time consuming
and can roughly double the runtime of the tool. When crosschecking many groups not
calculating the tumor-aware results can result in a significant speedup. Default value:
true. Possible values: {true, false}
--COMPRESSION_LEVEL <Integer> Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5.
--CREATE_INDEX <Boolean> Whether to create an index when writing VCF or coordinate sorted BAM output. Default
value: false. Possible values: {true, false}
--CREATE_MD5_FILE <Boolean> Whether to create an MD5 digest for any BAM or FASTQ files created. Default value:
false. Possible values: {true, false}
--CROSSCHECK_BY <DataType> Specifies which data-type should be used as the basic comparison unit. Fingerprints from
readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared.
Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP.
Possible values: {FILE, SAMPLE, LIBRARY, READGROUP}
--CROSSCHECK_MODE <CrosscheckMode>
An argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur.
Default value: CHECK_SAME_SAMPLE. CHECK_SAME_SAMPLE (In this mode, each sample in INPUT
will only be checked against a single corresponding sample in SECOND_INPUT. If a
corresponding sample cannot be found, the program will proceed, but report the missing
samples and return the value specified in EXIT_CODE_WHEN_MISMATCH. The corresponding
samples are those that equal each other, after possible renaming via INPUT_SAMPLE_MAP and
SECOND_INPUT_SAMPLE_MAP. In this mode CROSSCHECK_BY must be SAMPLE.)
CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the
samples in SECOND_INPUT.)
--EXIT_CODE_WHEN_MISMATCH <Integer>
When one or more mismatches between groups is detected, exit with this value instead of 0.
Default value: 1.
--EXIT_CODE_WHEN_NO_VALID_CHECKS <Integer>
When all LOD scores are zero, exit with this value. Default value: 1.
--EXPECT_ALL_GROUPS_TO_MATCH <Boolean>
Expect all groups' fingerprints to match, irrespective of their sample names. By default
(with this value set to false), groups (readgroups, libraries, files, or samples) with
different sample names are expected to mismatch, and those with the same sample name are
expected to match. Default value: false. Possible values: {true, false}
--GENOTYPING_ERROR_RATE <Double>
This argument is DEPRECATED (No longer used in fingerprint checking. Will be removed in a
future release.). Assumed genotyping error rate that provides a floor on the probability
that a genotype comes from the expected sample. Must be greater than zero. Default
value: 0.01.
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--INPUT_INDEX_MAP <File> A tsv with two columns and no header which maps the input files to corresponding indices;
to be used when index files are not located next to input files. First column must match
the list of inputs. Default value: null.
--INPUT_SAMPLE_FILE_MAP <File>A tsv with two columns representing the sample as it should be used for comparisons to
SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in
the second column). Need only to include the samples that change. Values in column 1
should be unique even in union with the remaining unmapped samples. Values in column 2
should be unique in the file. Will error if more than one sample is found in a file
(multi-sample VCF) pointed to in column 2. Should only be used in the presence of
SECOND_INPUT. Default value: null. Cannot be used in conjunction with argument(s)
INPUT_SAMPLE_MAP
--INPUT_SAMPLE_MAP <File> A tsv with two columns representing the sample as it appears in the INPUT data (in column
1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second
column). Need only include the samples that change. Values in column 1 should be unique.
Values in column 2 should be unique even in union with the remaining unmapped samples.
Should only be used with SECOND_INPUT. Default value: null. Cannot be used in
conjunction with argument(s) INPUT_SAMPLE_FILE_MAP
--LOD_THRESHOLD,-LOD <Double> If any two groups (with the same sample name) match with a LOD score lower than the
threshold the tool will exit with a non-zero code to indicate error. Program will also
exit with an error if it finds two groups with different sample name that match with a LOD
score greater than -LOD_THRESHOLD.
LOD score 0 means equal likelihood that the groups match vs. come from different
individuals, negative LOD score -N, mean 10^N time more likely that the groups are from
different individuals, and +N means 10^N times more likely that the groups are from the
same individual. Default value: 0.0.
--LOSS_OF_HET_RATE <Double> The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via
loss of heterozygosity) in the tumor (model assumes independent events, so this needs to
be larger than reality). Default value: 0.5.
--MATRIX_OUTPUT,-MO <File> Optional output file to write matrix of LOD scores to. This is less informative than the
metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of
Heterozygosity). It is however sometimes easier to use visually. Default value: null.
Cannot be used in conjunction with argument(s) SECOND_INPUT (SI)
--MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK <Double>
Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood
difference between the different values for the three possible genotypes). Default value:
3.0.
--MAX_RECORDS_IN_RAM <Integer>When writing files that need to be sorted, this will specify the number of records stored
in RAM before spilling to disk. Increasing this number reduces the number of file handles
needed to sort the file, and increases the amount of RAM needed. Default value: 500000.
--NUM_THREADS <Integer> The number of threads to use to process files and generate fingerprints. Default value:
1.
--OUTPUT,-O <File> Optional output file to write metrics to. Default is to write to stdout. Default value:
null.
--OUTPUT_ERRORS_ONLY <Boolean>If true, then only groups that do not relate to each other as expected will have their
LODs reported. Default value: false. Possible values: {true, false}
--QUIET <Boolean> Whether to suppress job-summary info on System.err. Default value: false. Possible
values: {true, false}
--REFERENCE_SEQUENCE,-R <PicardHtsPath>
Reference sequence file. Default value: null.
--REQUIRE_INDEX_FILES <Boolean>
A boolean value to determine whether input files should only be parsed if index files are
available. Without turning this option on, the tool will need to read through the entirety
of input files without index files either provided via the INPUT_INDEX_MAP or locally
accessible relative to the input, which significantly increases runtime. If set to true
and no index is found for a file, an exception will be thrown. This applies for both the
INPUT and SECOND_INPUT files. Default value: false. Possible values: {true, false}
--SAMPLE_INDIVIDUAL_MAP <File>A tsv with two columns representing the individual with which each sample is associated.
The first column is the sample id, and the second column is the associated individual id.
Values in the first column must be unique. If INPUT_SAMPLE_MAP or SECOND_INPUT_SAMPLE_MAP
is also specified, then the values in the first column of this file should be the sample
aliases specified in the second columns of INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP,
respectively. When this input is specified, expectations for matches will be based on the
equality or inequality of the individual ids associated with two samples, as opposed to
the sample ids themselves. Samples which are not listed in this file will have their
sample id used as their individual id, for the purposes of match expectations. This means
that one sample id could be used as the individual id for another sample, but not included
in the map itself, and these two samples would be considered to have come from the same
individual. Note that use of this parameter only affects labelling of matches and
mismatches as EXPECTED or UNEXPECTED. It has no affect on how data is grouped for
crosschecking. Default value: null.
--SECOND_INPUT,-SI <String> A second set of input files (or lists of files) with which to compare fingerprints. If
this option is provided the tool compares each sample in INPUT with the sample from
SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE
regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in
INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool
will proceed to check the matching samples, but report the missing samples and return a
non-zero error-code. This argument may be specified 0 or more times. Default value: null.
Cannot be used in conjunction with argument(s) MATRIX_OUTPUT (MO)
--SECOND_INPUT_INDEX_MAP <File>
A tsv with two columns and no header which maps the second input files to corresponding
indices; to be used when index files are not located next to second input files. First
column must match the list of second inputs. Default value: null.
--SECOND_INPUT_SAMPLE_MAP <File>
A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in
column 1) and the sample as it should be used for comparisons to INPUT (in the second
column). Note that in case of unrolling files (file-of-filenames) one would need to
reference the final file, i.e. the file that contains the genomic data. Need only include
the samples that change. Values in column 1 should be unique. Values in column 2 should be
unique even in union with the remaining unmapped samples. Should only be used with
SECOND_INPUT. Default value: null.
--TMP_DIR <File> One or more directories with space available to be used by this program for temporary
storage of working files This argument may be specified 0 or more times. Default value:
null.
--USE_JDK_DEFLATER,-use_jdk_deflater <Boolean>
Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default
value: false. Possible values: {true, false}
--USE_JDK_INFLATER,-use_jdk_inflater <Boolean>
Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default
value: false. Possible values: {true, false}
--VALIDATION_STRINGENCY <ValidationStringency>
Validation stringency for all SAM files read by this program. Setting stringency to
SILENT can improve performance when processing a BAM file in which variable-length data
(read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT.
Possible values: {STRICT, LENIENT, SILENT}
--VERBOSITY <LogLevel> Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
INFO, DEBUG}
--version <Boolean> display the version number for this tool Default value: false. Possible values: {true,
false}
Advanced Arguments:
--showHidden <Boolean> display hidden arguments Default value: false. Possible values: {true, false}
REFERENCE must be provided when using CRAM as input.
[Thu Apr 24 13:00:19 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --SAMPLE_INDIVIDUAL_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_NA12892_different_individuals.txt --OUTPUT /tmp/Fingerprinting7353869465277216765NA1291.SM.crosscheck_metrics --MATRIX_OUTPUT /tmp/Fingerprinting1748844647913590788NA1291.SM.matrix --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:19 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:19 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Cross-checking all SAMPLE against each other
INFO 2025-04-24 13:00:19 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:19 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:19 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --SAMPLE_INDIVIDUAL_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_NA12892_same_individual.txt --OUTPUT /tmp/Fingerprinting3381752252356372261NA1291.SM.crosscheck_metrics --MATRIX_OUTPUT /tmp/Fingerprinting9253282951111168926NA1291.SM.matrix --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:19 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:19 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Cross-checking all SAMPLE against each other
WARNING 2025-04-24 13:00:19 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:19 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:19 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --SAMPLE_INDIVIDUAL_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_NA12892_different_individuals.txt --OUTPUT /tmp/Fingerprinting10058562715077959503NA1291.SM.crosscheck_metrics --MATRIX_OUTPUT /tmp/Fingerprinting12828944427561534195NA1291.SM.matrix --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:19 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:19 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Cross-checking all SAMPLE against each other
WARNING 2025-04-24 13:00:19 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:19 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:19 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --SAMPLE_INDIVIDUAL_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_NA12892_same_individual.txt --OUTPUT /tmp/Fingerprinting2600691480226162528NA1291.SM.crosscheck_metrics --MATRIX_OUTPUT /tmp/Fingerprinting13472687210681574076NA1291.SM.matrix --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:19 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:19 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Cross-checking all SAMPLE against each other
INFO 2025-04-24 13:00:19 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:19 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:19 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --OUTPUT /tmp/Fingerprinting7108248356484675180NA1291.LB.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY LIBRARY --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:19 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:19 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:19 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:19 CrosscheckFingerprints Cross-checking all LIBRARY against each other
INFO 2025-04-24 13:00:20 CrosscheckFingerprints All LIBRARYs are related as expected.
[Thu Apr 24 13:00:20 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:20 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --OUTPUT /tmp/Fingerprinting6090828610673294348NA1291.LB.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY LIBRARY --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:20 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:20 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Cross-checking all LIBRARY against each other
INFO 2025-04-24 13:00:20 CrosscheckFingerprints All LIBRARYs are related as expected.
[Thu Apr 24 13:00:20 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:20 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --OUTPUT /tmp/Fingerprinting15701139533837092019NA1291.LB.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY LIBRARY --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:20 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:20 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Cross-checking all LIBRARY against each other
INFO 2025-04-24 13:00:20 CrosscheckFingerprints All LIBRARYs are related as expected.
[Thu Apr 24 13:00:20 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:20 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --OUTPUT /tmp/Fingerprinting11891070359109939964NA1291.LB.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY LIBRARY --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:20 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:20 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Cross-checking all LIBRARY against each other
INFO 2025-04-24 13:00:20 CrosscheckFingerprints All LIBRARYs are related as expected.
[Thu Apr 24 13:00:20 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:20 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam --OUTPUT /tmp/Fingerprinting17529881181829772957NA1291.LB.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY LIBRARY --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:20 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
WARNING 2025-04-24 13:00:20 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam)
INFO 2025-04-24 13:00:20 FingerprintChecker Processed files. 54 fingerprints found in map.
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Cross-checking all LIBRARY against each other
WARNING 2025-04-24 13:00:20 CrosscheckFingerprints 2 LIBRARYs did not relate as expected.
[Thu Apr 24 13:00:20 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:20 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam --OUTPUT /tmp/Fingerprinting12131848745473906016NA1291.LB.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY LIBRARY --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:20 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
WARNING 2025-04-24 13:00:20 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam)
INFO 2025-04-24 13:00:20 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Cross-checking all LIBRARY against each other
WARNING 2025-04-24 13:00:20 CrosscheckFingerprints 2 LIBRARYs did not relate as expected.
[Thu Apr 24 13:00:20 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:20 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam --OUTPUT /tmp/Fingerprinting4815655812189393201NA1291.LB.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY LIBRARY --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:20 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
WARNING 2025-04-24 13:00:20 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam)
INFO 2025-04-24 13:00:20 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Cross-checking all LIBRARY against each other
WARNING 2025-04-24 13:00:20 CrosscheckFingerprints 2 LIBRARYs did not relate as expected.
[Thu Apr 24 13:00:20 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:20 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam --OUTPUT /tmp/Fingerprinting8715569092322923182NA1291.LB.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY LIBRARY --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:20 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
WARNING 2025-04-24 13:00:20 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam)
INFO 2025-04-24 13:00:20 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Cross-checking all LIBRARY against each other
WARNING 2025-04-24 13:00:20 CrosscheckFingerprints 2 LIBRARYs did not relate as expected.
[Thu Apr 24 13:00:20 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:20 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam --OUTPUT /tmp/Fingerprinting10150741562911337429NA1291.LB.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY LIBRARY --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:20 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Fingerprinting 5 INPUT files.
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
WARNING 2025-04-24 13:00:20 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam)
INFO 2025-04-24 13:00:20 FingerprintChecker Processed files. 131 fingerprints found in map.
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Cross-checking all LIBRARY against each other
WARNING 2025-04-24 13:00:20 CrosscheckFingerprints 8 LIBRARYs did not relate as expected.
[Thu Apr 24 13:00:20 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:20 EDT 2025] ClusterCrosscheckMetrics --INPUT /tmp/Fingerprinting10150741562911337429NA1291.LB.crosscheck_metrics --OUTPUT /tmp/Fingerprinting15617906276485035903NA1291.LB.crosscheck_cluster_metrics --LOD_THRESHOLD 1.0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:20 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:00:20 EDT 2025] picard.fingerprint.ClusterCrosscheckMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:20 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --OUTPUT /tmp/Fingerprinting17104873528353394976NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:20 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:20 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:20 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:20 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:20 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --OUTPUT /tmp/Fingerprinting5502143688714974963NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:20 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:20 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:20 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:20 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:20 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --OUTPUT /tmp/Fingerprinting1641156094971311735NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:20 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:20 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:20 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:20 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:20 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --OUTPUT /tmp/Fingerprinting8368397862828291485NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:20 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:20 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:20 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:20 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:21 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:21 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:21 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --OUTPUT /tmp/Fingerprinting16017167962684579317NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:21 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:21 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:21 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:21 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:21 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:21 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:21 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --OUTPUT /tmp/Fingerprinting6391142503102961802NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:21 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:21 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:21 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:21 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:21 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:21 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:21 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --OUTPUT /tmp/Fingerprinting9854098828130411989NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:21 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:21 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:21 FingerprintChecker Processed files. 51 fingerprints found in map.
INFO 2025-04-24 13:00:21 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:21 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:21 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:21 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --OUTPUT /tmp/Fingerprinting6037517417548983907NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:21 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:21 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:21 FingerprintChecker Processed files. 51 fingerprints found in map.
INFO 2025-04-24 13:00:21 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:21 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:21 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:21 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --OUTPUT /tmp/Fingerprinting18208177916034608041NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:21 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:21 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:21 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:21 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:21 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:21 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:21 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --OUTPUT /tmp/Fingerprinting6252702029946978810NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:21 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:21 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:21 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:21 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:21 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:21 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:21 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --OUTPUT /tmp/Fingerprinting13769985834201743560NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:21 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:21 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:21 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:21 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:21 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:21 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:21 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --OUTPUT /tmp/Fingerprinting4659052140756313545NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:21 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:21 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:21 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:21 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:21 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:21 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:21 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --OUTPUT /tmp/Fingerprinting10601948256925489370NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:21 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:21 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:21 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:21 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:21 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:21 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:21 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --OUTPUT /tmp/Fingerprinting15932309208867713327NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:21 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:21 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:21 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:21 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:21 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:21 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:21 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --OUTPUT /tmp/Fingerprinting5824447706866464689NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:21 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:21 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:21 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:22 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Cross-checking all READGROUP against each other
WARNING 2025-04-24 13:00:22 CrosscheckFingerprints 84 READGROUPs did not relate as expected.
[Thu Apr 24 13:00:22 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:22 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --OUTPUT /tmp/Fingerprinting15612029878455613888NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:22 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:22 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:22 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:22 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Cross-checking all READGROUP against each other
WARNING 2025-04-24 13:00:22 CrosscheckFingerprints 64 READGROUPs did not relate as expected.
[Thu Apr 24 13:00:22 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:22 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --OUTPUT /tmp/Fingerprinting4791186157946807161NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:22 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:22 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:22 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:22 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Cross-checking all READGROUP against each other
WARNING 2025-04-24 13:00:22 CrosscheckFingerprints 138 READGROUPs did not relate as expected.
[Thu Apr 24 13:00:22 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:22 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --OUTPUT /tmp/Fingerprinting5195334507100703244NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:22 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:22 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:22 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:22 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Cross-checking all READGROUP against each other
WARNING 2025-04-24 13:00:22 CrosscheckFingerprints 108 READGROUPs did not relate as expected.
[Thu Apr 24 13:00:22 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:22 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --OUTPUT /tmp/Fingerprinting13724394363401194468NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:22 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:22 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:22 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:22 FingerprintChecker Processed files. 51 fingerprints found in map.
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:22 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:22 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:22 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --OUTPUT /tmp/Fingerprinting8622655869375411935NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:22 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:22 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:22 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:22 FingerprintChecker Processed files. 51 fingerprints found in map.
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:22 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:22 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:22 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --OUTPUT /tmp/Fingerprinting16014458954675927510NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:22 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:22 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:22 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:22 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Cross-checking all READGROUP against each other
WARNING 2025-04-24 13:00:22 CrosscheckFingerprints 188 READGROUPs did not relate as expected.
[Thu Apr 24 13:00:22 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:22 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --OUTPUT /tmp/Fingerprinting185991968737597903NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:22 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:22 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:22 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:22 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Cross-checking all READGROUP against each other
WARNING 2025-04-24 13:00:22 CrosscheckFingerprints 92 READGROUPs did not relate as expected.
[Thu Apr 24 13:00:22 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:22 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --OUTPUT /tmp/Fingerprinting15921572847873880979NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:22 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:22 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:22 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:22 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Cross-checking all READGROUP against each other
WARNING 2025-04-24 13:00:22 CrosscheckFingerprints 138 READGROUPs did not relate as expected.
[Thu Apr 24 13:00:22 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:22 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --OUTPUT /tmp/Fingerprinting10382517820332726324NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:22 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:22 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:22 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:22 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Cross-checking all READGROUP against each other
WARNING 2025-04-24 13:00:22 CrosscheckFingerprints 108 READGROUPs did not relate as expected.
[Thu Apr 24 13:00:22 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:22 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram --OUTPUT /tmp/Fingerprinting450452547452219156NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:22 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:22 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:22 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram)
INFO 2025-04-24 13:00:22 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:22 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:22 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:22 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram --OUTPUT /tmp/Fingerprinting12240961192427847301NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:22 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:22 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:23 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:23 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:23 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram --OUTPUT /tmp/Fingerprinting1332831602488524673NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:23 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:23 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:23 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:23 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram --OUTPUT /tmp/Fingerprinting18362412465221013532NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:23 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:23 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:23 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:23 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --OUTPUT /tmp/Fingerprinting12703924115171448954NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:23 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:23 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:23 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:23 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --OUTPUT /tmp/Fingerprinting5056270547537429825NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:23 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:23 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:23 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:23 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --OUTPUT /tmp/Fingerprinting18049178486250187967NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:23 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Processed files. 51 fingerprints found in map.
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:23 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:23 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:23 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --OUTPUT /tmp/Fingerprinting346721328049233199NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:23 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Processed files. 51 fingerprints found in map.
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:23 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:23 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:23 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram --OUTPUT /tmp/Fingerprinting1056474070090013640NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:23 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:23 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:23 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:23 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram --OUTPUT /tmp/Fingerprinting5211162916793876346NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:23 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:23 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:23 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:23 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --OUTPUT /tmp/Fingerprinting4247333460104866472NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:23 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:23 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:23 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:23 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --OUTPUT /tmp/Fingerprinting358118112364091030NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:23 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:23 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:23 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:23 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram --OUTPUT /tmp/Fingerprinting13784913911363353171NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:23 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:23 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:23 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:23 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram --OUTPUT /tmp/Fingerprinting10445829542262659530NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:23 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:23 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:23 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:23 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram --OUTPUT /tmp/Fingerprinting11833543103179294702NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:23 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram)
INFO 2025-04-24 13:00:23 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:23 CrosscheckFingerprints Cross-checking all READGROUP against each other
WARNING 2025-04-24 13:00:23 CrosscheckFingerprints 58 READGROUPs did not relate as expected.
[Thu Apr 24 13:00:23 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:24 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram --OUTPUT /tmp/Fingerprinting10820640345561382830NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram)
INFO 2025-04-24 13:00:24 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Cross-checking all READGROUP against each other
WARNING 2025-04-24 13:00:24 CrosscheckFingerprints 44 READGROUPs did not relate as expected.
[Thu Apr 24 13:00:24 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:24 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --OUTPUT /tmp/Fingerprinting7045835248827882259NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:24 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Cross-checking all READGROUP against each other
WARNING 2025-04-24 13:00:24 CrosscheckFingerprints 48 READGROUPs did not relate as expected.
[Thu Apr 24 13:00:24 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:24 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --OUTPUT /tmp/Fingerprinting9961590801956338719NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:24 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Cross-checking all READGROUP against each other
WARNING 2025-04-24 13:00:24 CrosscheckFingerprints 36 READGROUPs did not relate as expected.
[Thu Apr 24 13:00:24 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:24 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --OUTPUT /tmp/Fingerprinting5509351264736654928NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram)
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:24 FingerprintChecker Processed files. 51 fingerprints found in map.
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:24 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:24 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:24 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --OUTPUT /tmp/Fingerprinting12077147444702435727NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam9654461037721150168.cram)
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:24 FingerprintChecker Processed files. 51 fingerprints found in map.
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:24 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:24 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:24 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram --OUTPUT /tmp/Fingerprinting8115102030543177969NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram)
INFO 2025-04-24 13:00:24 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Cross-checking all READGROUP against each other
WARNING 2025-04-24 13:00:24 CrosscheckFingerprints 8 READGROUPs did not relate as expected.
[Thu Apr 24 13:00:24 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:24 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram --OUTPUT /tmp/Fingerprinting12750133197030998337NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam6161685524065059823.cram)
INFO 2025-04-24 13:00:24 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Cross-checking all READGROUP against each other
WARNING 2025-04-24 13:00:24 CrosscheckFingerprints 2 READGROUPs did not relate as expected.
[Thu Apr 24 13:00:24 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:24 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --OUTPUT /tmp/Fingerprinting3570113680765859474NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:24 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Cross-checking all READGROUP against each other
WARNING 2025-04-24 13:00:24 CrosscheckFingerprints 48 READGROUPs did not relate as expected.
[Thu Apr 24 13:00:24 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:24 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram --INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram --OUTPUT /tmp/Fingerprinting9001980275328095870NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.short_dictionary.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --REFERENCE_SEQUENCE testdata/picard/fingerprint/reference.shifted.for.crams.fasta --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam1273052142615017970.cram)
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam4973888153311302428.cram)
INFO 2025-04-24 13:00:24 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Cross-checking all READGROUP against each other
WARNING 2025-04-24 13:00:24 CrosscheckFingerprints 36 READGROUPs did not relate as expected.
[Thu Apr 24 13:00:24 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:24 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --OUTPUT /tmp/Fingerprinting7290333048330952382NA1291.SM.crosscheck_metrics --MATRIX_OUTPUT /tmp/Fingerprinting3029585259978649NA1291.SM.matrix --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:24 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Cross-checking all SAMPLE against each other
INFO 2025-04-24 13:00:24 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:24 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:24 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --OUTPUT /tmp/Fingerprinting5118613788680772550NA1291.SM.crosscheck_metrics --MATRIX_OUTPUT /tmp/Fingerprinting994002044189476598NA1291.SM.matrix --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:24 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Cross-checking all SAMPLE against each other
INFO 2025-04-24 13:00:24 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:24 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:24 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --OUTPUT /tmp/Fingerprinting11607951623079864969NA1291.SM.crosscheck_metrics --MATRIX_OUTPUT /tmp/Fingerprinting2534382520318569202NA1291.SM.matrix --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:24 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Cross-checking all SAMPLE against each other
INFO 2025-04-24 13:00:24 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:24 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:24 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --OUTPUT /tmp/Fingerprinting6910450578569547116NA1291.SM.crosscheck_metrics --MATRIX_OUTPUT /tmp/Fingerprinting1898618174563671347NA1291.SM.matrix --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:24 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Cross-checking all SAMPLE against each other
INFO 2025-04-24 13:00:24 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:24 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:24 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --OUTPUT /tmp/Fingerprinting12877243355537032347NA1291.SM.crosscheck_metrics --MATRIX_OUTPUT /tmp/Fingerprinting10248718791272806127NA1291.SM.matrix --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:24 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Cross-checking all SAMPLE against each other
WARNING 2025-04-24 13:00:24 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:24 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:24 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --OUTPUT /tmp/Fingerprinting10825365875982033513NA1291.SM.crosscheck_metrics --MATRIX_OUTPUT /tmp/Fingerprinting7747607334984490848NA1291.SM.matrix --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:24 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Cross-checking all SAMPLE against each other
INFO 2025-04-24 13:00:24 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:24 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:24 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --OUTPUT /tmp/Fingerprinting5818329160582680798NA1291.SM.crosscheck_metrics --MATRIX_OUTPUT /tmp/Fingerprinting14192461939108961753NA1291.SM.matrix --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:24 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:24 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:24 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 54 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Cross-checking all SAMPLE against each other
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --OUTPUT /tmp/Fingerprinting9363422362060805538NA1291.Sources.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Cross-checking all FILE against each other
INFO 2025-04-24 13:00:25 CrosscheckFingerprints All FILEs are related as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --OUTPUT /tmp/Fingerprinting16812775410039161692NA1291.Sources.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 51 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Cross-checking all FILE against each other
INFO 2025-04-24 13:00:25 CrosscheckFingerprints All FILEs are related as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --OUTPUT /tmp/Fingerprinting296839965474364167NA1291.Sources.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Cross-checking all FILE against each other
INFO 2025-04-24 13:00:25 CrosscheckFingerprints All FILEs are related as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --OUTPUT /tmp/Fingerprinting606376152034744271NA1291.Sources.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Cross-checking all FILE against each other
INFO 2025-04-24 13:00:25 CrosscheckFingerprints All FILEs are related as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --OUTPUT /tmp/Fingerprinting14749829061650643959NA1291.Sources.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Cross-checking all FILE against each other
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints 2 FILEs did not relate as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --OUTPUT /tmp/Fingerprinting3819485780085460753NA1291.Sources.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Cross-checking all FILE against each other
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints 2 FILEs did not relate as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --OUTPUT /tmp/Fingerprinting1680827695730597133NA1291.Sources.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Cross-checking all FILE against each other
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints 2 FILEs did not relate as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --OUTPUT /tmp/Fingerprinting14010736637673974315NA1291.Sources.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 54 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Cross-checking all FILE against each other
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints 2 FILEs did not relate as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.vcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12892.vcf.gz --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.g.vcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12892.g.vcf --INPUT_INDEX_MAP /tmp/input_index_map8344825935591712455.tsv --REQUIRE_INDEX_FILES true --OUTPUT /tmp/Fingerprinting3087044552740187034test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 4 INPUT files.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Forcing index files to be present for fingerprinting input files.
INFO 2025-04-24 13:00:25 FingerprintChecker Using explicit index provided for /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.vcf
INFO 2025-04-24 13:00:25 FingerprintChecker Using explicit index provided for /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12892.vcf.gz
INFO 2025-04-24 13:00:25 FingerprintChecker Using explicit index provided for /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.g.vcf
INFO 2025-04-24 13:00:25 FingerprintChecker Using explicit index provided for /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12892.g.vcf
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 4 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Cross-checking all FILE against each other
INFO 2025-04-24 13:00:25 CrosscheckFingerprints All FILEs are related as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891andNA12892.vcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.fp.vcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12892.vcf.gz --INPUT_INDEX_MAP /tmp/input_index_map3229765959272686190.tsv --REQUIRE_INDEX_FILES true --OUTPUT /tmp/Fingerprinting16193645753660531318test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 3 INPUT files.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Forcing index files to be present for fingerprinting input files.
INFO 2025-04-24 13:00:25 FingerprintChecker Using explicit index provided for /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891andNA12892.vcf
INFO 2025-04-24 13:00:25 FingerprintChecker Using explicit index provided for /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.fp.vcf
INFO 2025-04-24 13:00:25 FingerprintChecker Using explicit index provided for /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12892.vcf.gz
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 4 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Cross-checking all FILE against each other
INFO 2025-04-24 13:00:25 CrosscheckFingerprints All FILEs are related as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r1.bam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12892.over.fingerprints.r1.bam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r2.bam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12892.over.fingerprints.r2.bam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.g.vcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12892.g.vcf --INPUT_INDEX_MAP /tmp/input_index_map5342862463735358486.tsv --REQUIRE_INDEX_FILES true --OUTPUT /tmp/Fingerprinting6160898114428653151test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 6 INPUT files.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Forcing index files to be present for fingerprinting input files.
INFO 2025-04-24 13:00:25 FingerprintChecker Using explicit index provided for /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r1.bam
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r1.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Using explicit index provided for /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12892.over.fingerprints.r1.bam
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12892.over.fingerprints.r1.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Using explicit index provided for /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r2.bam
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r2.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Using explicit index provided for /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12892.over.fingerprints.r2.bam
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12892.over.fingerprints.r2.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Using explicit index provided for /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.g.vcf
INFO 2025-04-24 13:00:25 FingerprintChecker Using explicit index provided for /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12892.g.vcf
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 106 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Cross-checking all FILE against each other
INFO 2025-04-24 13:00:25 CrosscheckFingerprints All FILEs are related as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r1.bam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12892.over.fingerprints.r1.bam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r2.bam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12892.over.fingerprints.r2.bam --INPUT_INDEX_MAP /tmp/input_index_map2855779374756157649.tsv --REQUIRE_INDEX_FILES true --OUTPUT /tmp/Fingerprinting9476371971815968773test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 4 INPUT files.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Forcing index files to be present for fingerprinting input files.
INFO 2025-04-24 13:00:25 FingerprintChecker Using explicit index provided for /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r1.bam
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r1.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Using explicit index provided for /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12892.over.fingerprints.r1.bam
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12892.over.fingerprints.r1.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Using explicit index provided for /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r2.bam
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r2.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Using explicit index provided for /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12892.over.fingerprints.r2.bam
INFO 2025-04-24 13:00:25 FingerprintChecker Reading an indexed file (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12892.over.fingerprints.r2.bam)
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 104 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Cross-checking all FILE against each other
INFO 2025-04-24 13:00:25 CrosscheckFingerprints All FILEs are related as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.vcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.fp.vcf --INPUT_INDEX_MAP /tmp/input_index_map2905607309586043530.tsv --REQUIRE_INDEX_FILES true --OUTPUT /tmp/Fingerprinting16671218766776864124test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Forcing index files to be present for fingerprinting input files.
INFO 2025-04-24 13:00:25 FingerprintChecker Using explicit index provided for /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.vcf
WARNING 2025-04-24 13:00:25 FingerprintChecker Index map file provided, but no explicit index provided for /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.fp.vcf
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r1.bam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r2.bam --INPUT_INDEX_MAP /tmp/input_index_map16117218808207419400.tsv --REQUIRE_INDEX_FILES true --OUTPUT /tmp/Fingerprinting2624528486683346884test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Forcing index files to be present for fingerprinting input files.
WARNING 2025-04-24 13:00:25 FingerprintChecker Index map file provided, but no explicit index provided for /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r1.bam
WARNING 2025-04-24 13:00:25 FingerprintChecker Index map file provided, but no explicit index provided for /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/index_test/files/NA12891.over.fingerprints.r2.bam
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --SECOND_INPUT /tmp/fingerprint8888332551852945861.vcf --CROSSCHECK_MODE CHECK_SAME_SAMPLE --OUTPUT /tmp/Fingerprinting.comparison9602133953654469498crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
ERROR 2025-04-24 13:00:25 CrosscheckFingerprints sample NA12892 is missing from LEFT group
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --SECOND_INPUT /tmp/fingerprint14467713583919176379.vcf --CROSSCHECK_MODE CHECK_SAME_SAMPLE --OUTPUT /tmp/Fingerprinting.comparison9602133953654469498crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
ERROR 2025-04-24 13:00:25 CrosscheckFingerprints sample NA12892 is missing from RIGHT group
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12891.vcf --SECOND_INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf --CROSSCHECK_MODE CHECK_SAME_SAMPLE --OUTPUT /tmp/Fingerprinting.comparison7534398737600563692crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 INPUT files.
WARNING 2025-04-24 13:00:25 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
WARNING 2025-04-24 13:00:25 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
ERROR 2025-04-24 13:00:25 CrosscheckFingerprints sample NA12892 is missing from LEFT group
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf --SECOND_INPUT testdata/picard/fingerprint/NA12891.vcf --CROSSCHECK_MODE CHECK_SAME_SAMPLE --OUTPUT /tmp/Fingerprinting.comparison7534398737600563692crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 INPUT files.
WARNING 2025-04-24 13:00:25 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
WARNING 2025-04-24 13:00:25 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
ERROR 2025-04-24 13:00:25 CrosscheckFingerprints sample NA12892 is missing from RIGHT group
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint3521993417099577267.vcf --SECOND_INPUT /tmp/fingerprint8888332551852945861.vcf --CROSSCHECK_MODE CHECK_SAME_SAMPLE --OUTPUT /tmp/Fingerprinting.comparison2422044083985807086crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
ERROR 2025-04-24 13:00:25 CrosscheckFingerprints sample NA12891 from LEFT group was not fingerprinted. Probably there are no reads/variants at fingerprinting sites.
ERROR 2025-04-24 13:00:25 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --SECOND_INPUT /tmp/fingerprint3521993417099577267.vcf --CROSSCHECK_MODE CHECK_SAME_SAMPLE --OUTPUT /tmp/Fingerprinting.comparison2422044083985807086crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
ERROR 2025-04-24 13:00:25 CrosscheckFingerprints sample NA12891 from RIGHT group was not fingerprinted. Probably there are no reads/variants at fingerprinting sites.
ERROR 2025-04-24 13:00:25 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf --SECOND_INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf --CROSSCHECK_MODE CHECK_SAME_SAMPLE --OUTPUT /tmp/Fingerprinting.comparison16302855479952840123crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 INPUT files.
WARNING 2025-04-24 13:00:25 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf going to read through it all.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
WARNING 2025-04-24 13:00:25 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
ERROR 2025-04-24 13:00:25 CrosscheckFingerprints sample NA12891 from LEFT group was not fingerprinted. Probably there are no reads/variants at fingerprinting sites.
ERROR 2025-04-24 13:00:25 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf --SECOND_INPUT testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf --CROSSCHECK_MODE CHECK_SAME_SAMPLE --OUTPUT /tmp/Fingerprinting.comparison16302855479952840123crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 INPUT files.
WARNING 2025-04-24 13:00:25 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
WARNING 2025-04-24 13:00:25 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf going to read through it all.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
ERROR 2025-04-24 13:00:25 CrosscheckFingerprints sample NA12891 from RIGHT group was not fingerprinted. Probably there are no reads/variants at fingerprinting sites.
ERROR 2025-04-24 13:00:25 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --SECOND_INPUT /tmp/fingerprint8888332551852945861.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison15998237403239689691crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --SECOND_INPUT /tmp/fingerprint14467713583919176379.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison15998237403239689691crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12891.vcf --SECOND_INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison14429569012502440484crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 INPUT files.
WARNING 2025-04-24 13:00:25 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
WARNING 2025-04-24 13:00:25 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf --SECOND_INPUT testdata/picard/fingerprint/NA12891.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison14429569012502440484crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 INPUT files.
WARNING 2025-04-24 13:00:25 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
WARNING 2025-04-24 13:00:25 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint3521993417099577267.vcf --SECOND_INPUT /tmp/fingerprint8888332551852945861.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison6075220183703324054crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints NA12891 was not fingerprinted in LEFT group. It probably has no calls/reads overlapping fingerprinting sites.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --SECOND_INPUT /tmp/fingerprint3521993417099577267.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison6075220183703324054crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints NA12891 was not fingerprinted in RIGHT group. It probably has no calls/reads overlapping fingerprinting sites.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf --SECOND_INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison3813459309988783501crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 INPUT files.
WARNING 2025-04-24 13:00:25 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf going to read through it all.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
WARNING 2025-04-24 13:00:25 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints NA12891 was not fingerprinted in LEFT group. It probably has no calls/reads overlapping fingerprinting sites.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf --SECOND_INPUT testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison3813459309988783501crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:25 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 INPUT files.
WARNING 2025-04-24 13:00:25 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
WARNING 2025-04-24 13:00:25 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf going to read through it all.
INFO 2025-04-24 13:00:25 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:25 CrosscheckFingerprints NA12891 was not fingerprinted in RIGHT group. It probably has no calls/reads overlapping fingerprinting sites.
INFO 2025-04-24 13:00:25 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:25 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:25 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint10453431263314259543.vcf --SECOND_INPUT /tmp/fingerprint8888332551852945861.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison9706320697394493407crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:26 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:26 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:26 CrosscheckFingerprints NA12891 was not fingerprinted in LEFT group. It probably has no calls/reads overlapping fingerprinting sites.
ERROR 2025-04-24 13:00:26 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites
[Thu Apr 24 13:00:26 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:26 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --SECOND_INPUT /tmp/fingerprint10453431263314259543.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison9706320697394493407crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:26 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:26 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:26 CrosscheckFingerprints NA12891 was not fingerprinted in RIGHT group. It probably has no calls/reads overlapping fingerprinting sites.
ERROR 2025-04-24 13:00:26 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites
[Thu Apr 24 13:00:26 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:26 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12891.no.fp.sites.vcf --SECOND_INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison12973503088130707724crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:26 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:26 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 1 INPUT files.
WARNING 2025-04-24 13:00:26 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.no.fp.sites.vcf going to read through it all.
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
WARNING 2025-04-24 13:00:26 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all.
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:26 CrosscheckFingerprints NA12891 was not fingerprinted in LEFT group. It probably has no calls/reads overlapping fingerprinting sites.
ERROR 2025-04-24 13:00:26 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites
[Thu Apr 24 13:00:26 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:26 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf --SECOND_INPUT testdata/picard/fingerprint/NA12891.no.fp.sites.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison12973503088130707724crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:26 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:26 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 1 INPUT files.
WARNING 2025-04-24 13:00:26 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all.
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
WARNING 2025-04-24 13:00:26 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.no.fp.sites.vcf going to read through it all.
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:26 CrosscheckFingerprints NA12891 was not fingerprinted in RIGHT group. It probably has no calls/reads overlapping fingerprinting sites.
ERROR 2025-04-24 13:00:26 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites
[Thu Apr 24 13:00:26 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:26 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --CROSSCHECK_MODE CHECK_SAME_SAMPLE --OUTPUT /tmp/Fingerprinting.comparison8302668118259553122crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:26 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:26 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:26 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:26 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 25 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:26 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:26 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
ERROR 2025-04-24 13:00:26 CrosscheckFingerprints sample NA12891 is missing from LEFT group
WARNING 2025-04-24 13:00:26 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:26 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:26 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --SECOND_INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --CROSSCHECK_MODE CHECK_SAME_SAMPLE --OUTPUT /tmp/Fingerprinting.comparison8302668118259553122crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:26 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:26 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:26 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:26 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:26 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:26 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 25 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
ERROR 2025-04-24 13:00:26 CrosscheckFingerprints sample NA12891 is missing from RIGHT group
WARNING 2025-04-24 13:00:26 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:26 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:26 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam --SECOND_INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam --SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam --CROSSCHECK_MODE CHECK_SAME_SAMPLE --OUTPUT /tmp/Fingerprinting.comparison7012104166108015614crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:26 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:26 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:26 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 1 INPUT files.
WARNING 2025-04-24 13:00:26 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 25 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
WARNING 2025-04-24 13:00:26 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam)
WARNING 2025-04-24 13:00:26 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam)
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
ERROR 2025-04-24 13:00:26 CrosscheckFingerprints sample NA12891 is missing from LEFT group
WARNING 2025-04-24 13:00:26 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:26 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:26 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam --INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam --SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam --CROSSCHECK_MODE CHECK_SAME_SAMPLE --OUTPUT /tmp/Fingerprinting.comparison7012104166108015614crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:26 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:26 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:26 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 2 INPUT files.
WARNING 2025-04-24 13:00:26 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam)
WARNING 2025-04-24 13:00:26 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam)
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
WARNING 2025-04-24 13:00:26 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 25 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
ERROR 2025-04-24 13:00:26 CrosscheckFingerprints sample NA12891 is missing from RIGHT group
WARNING 2025-04-24 13:00:26 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:26 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:26 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.not.over.fingerprints.r1.sam9259756035576409424.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --CROSSCHECK_MODE CHECK_SAME_SAMPLE --OUTPUT /tmp/Fingerprinting.comparison9328287551816086440crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:26 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:26 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:26 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:26 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.not.over.fingerprints.r1.sam9259756035576409424.bam)
INFO 2025-04-24 13:00:26 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:26 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:26 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
ERROR 2025-04-24 13:00:26 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples
WARNING 2025-04-24 13:00:26 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:26 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:26 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --SECOND_INPUT /tmp/NA12891.not.over.fingerprints.r1.sam9259756035576409424.bam --SECOND_INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --CROSSCHECK_MODE CHECK_SAME_SAMPLE --OUTPUT /tmp/Fingerprinting.comparison9328287551816086440crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:26 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:26 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:26 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:26 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:26 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:26 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.not.over.fingerprints.r1.sam9259756035576409424.bam)
INFO 2025-04-24 13:00:26 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
ERROR 2025-04-24 13:00:26 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples
WARNING 2025-04-24 13:00:26 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:26 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:26 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam --INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam --SECOND_INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam --SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam --CROSSCHECK_MODE CHECK_SAME_SAMPLE --OUTPUT /tmp/Fingerprinting.comparison17816650990575850355crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:26 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:26 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:26 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 2 INPUT files.
WARNING 2025-04-24 13:00:26 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam)
WARNING 2025-04-24 13:00:26 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
WARNING 2025-04-24 13:00:26 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam)
WARNING 2025-04-24 13:00:26 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam)
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
ERROR 2025-04-24 13:00:26 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples
WARNING 2025-04-24 13:00:26 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:26 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:26 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam --INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam --SECOND_INPUT testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam --SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam --CROSSCHECK_MODE CHECK_SAME_SAMPLE --OUTPUT /tmp/Fingerprinting.comparison17816650990575850355crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --REQUIRE_INDEX_FILES false --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:26 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:26 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT.
WARNING 2025-04-24 13:00:26 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 2 INPUT files.
WARNING 2025-04-24 13:00:26 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam)
WARNING 2025-04-24 13:00:26 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam)
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
WARNING 2025-04-24 13:00:26 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam)
WARNING 2025-04-24 13:00:26 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT.
ERROR 2025-04-24 13:00:26 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples
WARNING 2025-04-24 13:00:26 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:26 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:26 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison13456511349653672737crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:26 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:26 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:26 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 25 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:26 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:26 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:26 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:26 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --SECOND_INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison13456511349653672737crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:26 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:26 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:26 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:26 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:26 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:26 FingerprintChecker Processed files. 25 fingerprints found in map.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:26 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:26 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam --SECOND_INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam --SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison11399980068785015474crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:26 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:26 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:26 CrosscheckFingerprints Fingerprinting 1 INPUT files.
WARNING 2025-04-24 13:00:26 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 25 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
WARNING 2025-04-24 13:00:27 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam)
WARNING 2025-04-24 13:00:27 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:27 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:27 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam --INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam --SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison11399980068785015474crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:27 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:27 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 2 INPUT files.
WARNING 2025-04-24 13:00:27 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam)
WARNING 2025-04-24 13:00:27 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
WARNING 2025-04-24 13:00:27 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 25 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:27 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:27 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.not.over.fingerprints.r1.sam9259756035576409424.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison7195381501242542723crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:27 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:27 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:27 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.not.over.fingerprints.r1.sam9259756035576409424.bam)
INFO 2025-04-24 13:00:27 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:27 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:27 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:27 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:27 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --SECOND_INPUT /tmp/NA12891.not.over.fingerprints.r1.sam9259756035576409424.bam --SECOND_INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison7195381501242542723crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:27 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:27 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:27 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:27 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:27 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.not.over.fingerprints.r1.sam9259756035576409424.bam)
INFO 2025-04-24 13:00:27 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:27 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:27 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam --INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam --SECOND_INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam --SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison5434577385125643595crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:27 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:27 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 2 INPUT files.
WARNING 2025-04-24 13:00:27 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam)
WARNING 2025-04-24 13:00:27 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
WARNING 2025-04-24 13:00:27 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam)
WARNING 2025-04-24 13:00:27 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:27 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:27 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam --INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam --SECOND_INPUT testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam --SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison5434577385125643595crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:27 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:27 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 2 INPUT files.
WARNING 2025-04-24 13:00:27 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam)
WARNING 2025-04-24 13:00:27 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
WARNING 2025-04-24 13:00:27 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam)
WARNING 2025-04-24 13:00:27 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:27 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:27 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.not.over.fingerprints.r1.sam9259756035576409424.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison12838766488697476793crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:27 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:27 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:27 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.not.over.fingerprints.r1.sam9259756035576409424.bam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:27 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:27 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
ERROR 2025-04-24 13:00:27 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites
[Thu Apr 24 13:00:27 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:27 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --SECOND_INPUT /tmp/NA12891.not.over.fingerprints.r1.sam9259756035576409424.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison12838766488697476793crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:27 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:27 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:27 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:27 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:27 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.not.over.fingerprints.r1.sam9259756035576409424.bam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
ERROR 2025-04-24 13:00:27 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites
[Thu Apr 24 13:00:27 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:27 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam --SECOND_INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam --SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison11634742963123989611crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:27 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:27 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 1 INPUT files.
WARNING 2025-04-24 13:00:27 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
WARNING 2025-04-24 13:00:27 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam)
WARNING 2025-04-24 13:00:27 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
ERROR 2025-04-24 13:00:27 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites
[Thu Apr 24 13:00:27 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:27 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam --INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam --SECOND_INPUT testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison11634742963123989611crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:27 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:27 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 2 INPUT files.
WARNING 2025-04-24 13:00:27 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam)
WARNING 2025-04-24 13:00:27 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
WARNING 2025-04-24 13:00:27 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
ERROR 2025-04-24 13:00:27 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites
[Thu Apr 24 13:00:27 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:27 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam1104553196726432233.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison12600263174694214985crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY READGROUP --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:27 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:27 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam1104553196726432233.bam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:27 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:27 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:27 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison6434289527849375017crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY READGROUP --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:27 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 1 INPUT files.
WARNING 2025-04-24 13:00:27 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:27 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:27 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:27 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.not.over.fingerprints.r1.sam9259756035576409424.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison7826274500447999627crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY READGROUP --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:27 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:27 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.not.over.fingerprints.r1.sam9259756035576409424.bam)
INFO 2025-04-24 13:00:27 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:27 CrosscheckFingerprints Cross-checking all READGROUP against each other
ERROR 2025-04-24 13:00:28 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites
[Thu Apr 24 13:00:28 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:28 EDT 2025] CrosscheckFingerprints --INPUT testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting.comparison16461304293489969580crosscheck_metrics --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY READGROUP --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 1 INPUT files.
WARNING 2025-04-24 13:00:28 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam)
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Cross-checking all READGROUP against each other
ERROR 2025-04-24 13:00:28 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites
[Thu Apr 24 13:00:28 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:28 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --SECOND_INPUT /tmp/fingerprint6120156480145075008.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting15794823203865725883test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:28 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:28 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:28 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --SECOND_INPUT /tmp/fingerprint6120156480145075008.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting6958330025765444390test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:28 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:28 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:28 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint3579231993969887448.vcf --INPUT /tmp/fingerprint15439106532535527298.vcf --INPUT /tmp/fingerprint11888033466904643149.vcf --SECOND_INPUT /tmp/fingerprint6120156480145075008.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting12347197631408252500test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:28 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 3 INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 6 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:28 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:28 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint11230533161859790849.vcf --INPUT /tmp/fingerprint14467713583919176379.vcf --SECOND_INPUT /tmp/fingerprint6120156480145075008.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting17885294894254839427test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:28 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:28 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:28 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:28 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --SECOND_INPUT /tmp/fingerprint10019297239983490355.vcf --SECOND_INPUT /tmp/fingerprint602062117778355363.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting8658025423285651717test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:28 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:28 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:28 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --SECOND_INPUT /tmp/fingerprint10019297239983490355.vcf --SECOND_INPUT /tmp/fingerprint602062117778355363.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting13548086541938201524test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:28 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:28 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:28 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --SECOND_INPUT /tmp/fingerprint6120156480145075008.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting6918539388659848740test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:28 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:28 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:28 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --SECOND_INPUT /tmp/fingerprint6120156480145075008.vcf --SECOND_INPUT /tmp/fingerprint11230533161859790849.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting1430933328963495966test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:28 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:28 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:28 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:28 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint3579231993969887448.vcf --INPUT /tmp/fingerprint15439106532535527298.vcf --INPUT /tmp/fingerprint11888033466904643149.vcf --SECOND_INPUT /tmp/fingerprint10019297239983490355.vcf --SECOND_INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting16867436527290659746test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:28 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 3 INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 6 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 26 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:28 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:28 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --SECOND_INPUT /tmp/fingerprint6120156480145075008.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting16843471921653534231test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:28 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 4 INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 104 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:28 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:28 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --SECOND_INPUT /tmp/fingerprint6120156480145075008.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting1585609189429473676test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:28 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 54 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:28 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:28 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:28 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/fingerprint602062117778355363.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting17918660785244535420test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:28 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 26 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:28 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:28 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/fingerprint4717421520942808288.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting3924250656995712596test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:28 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 28 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:28 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:28 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:28 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --SECOND_INPUT /tmp/fingerprint10019297239983490355.vcf --SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting6443486596367944274test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:28 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 28 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:28 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:28 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:28 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --SECOND_INPUT /tmp/fingerprint10019297239983490355.vcf --SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting10046470748601888529test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:28 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 28 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:28 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:28 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:28 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting1213292498232112503test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:28 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:28 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:28 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting15681939914927747388test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:28 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 26 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:28 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:28 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting2763044794283222738test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:28 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:28 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:28 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting12779874708855456655test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:28 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 54 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:28 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:28 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:28 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting2912819215671018149test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:28 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:28 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:28 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:28 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 54 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:29 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --SECOND_INPUT /tmp/fingerprint7827008760857261976.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting926878822120375556test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:29 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting3272610318901066112test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting1592884592767091427test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint3579231993969887448.vcf --INPUT /tmp/fingerprint15439106532535527298.vcf --INPUT /tmp/fingerprint11888033466904643149.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting12819413388943903054test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 3 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 6 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint11230533161859790849.vcf --INPUT /tmp/fingerprint14467713583919176379.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting12285476709996203387test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:29 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --SECOND_INPUT /tmp/fingerprint602062117778355363.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting1567454838033943170test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --SECOND_INPUT /tmp/fingerprint602062117778355363.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting6333017534961642828test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting5039507984518098138test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --SECOND_INPUT /tmp/fingerprint11230533161859790849.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting15791844880240286169test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:29 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint3579231993969887448.vcf --INPUT /tmp/fingerprint15439106532535527298.vcf --INPUT /tmp/fingerprint11888033466904643149.vcf --SECOND_INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting2424928012299527471test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 3 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 6 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 25 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting10950374293769568363test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 4 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 104 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting4749520630366429408test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 54 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:29 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/fingerprint602062117778355363.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting6965718130015121624test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 25 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/fingerprint4717421520942808288.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting461104007916061089test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:29 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint602062117778355363.vcf --SECOND_INPUT /tmp/fingerprint10019297239983490355.vcf --SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting12593810726779659780test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 28 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:29 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting10118913779348738042test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:29 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting6392480750302204440test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 25 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting16574794494750547074test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 25 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 26 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting12349655729109848214test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 26 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting15490887670154773439test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:29 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam --SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting4551730577066855130test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 25 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam6489948231100895040.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 54 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:29 CrosscheckFingerprints 1 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint602062117778355363.vcf --SECOND_INPUT /tmp/fingerprint7827008760857261976.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting14305154664786299324test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --INPUT_SAMPLE_FILE_MAP /tmp/map16724391013107926805.txt --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting16715082984639443389test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:29 FingerprintChecker Processed files. 26 fingerprints found in map.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:29 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:29 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --INPUT_SAMPLE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NotThere_to_NA12891.txt --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting11760293076212405020test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:29 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:29 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:29 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:29 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 25 fingerprints found in map.
WARNING 2025-04-24 13:00:30 CrosscheckFingerprints Some samples in first column in the INPUT_SAMPLE_MAP were not present as samples in fingerprinted file: [NotThere].
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:30 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:30 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --SECOND_INPUT_SAMPLE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NotThere_to_NA12891.txt --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting13415108499644077601test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:30 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:30 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 25 fingerprints found in map.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 52 fingerprints found in map.
WARNING 2025-04-24 13:00:30 CrosscheckFingerprints Some samples in first column in the SECOND_INPUT_SAMPLE_MAP were not present as samples in fingerprinted file: [NotThere].
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:30 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:30 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam --INPUT_SAMPLE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NotThere_to_NA12891.txt --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam --SECOND_INPUT_SAMPLE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NotThere_to_NA12891.txt --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting4791858892226996886test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:30 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:30 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam12555386904253955187.bam)
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 25 fingerprints found in map.
WARNING 2025-04-24 13:00:30 CrosscheckFingerprints Some samples in first column in the INPUT_SAMPLE_MAP were not present as samples in fingerprinted file: [NotThere].
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam9083254664436795996.bam)
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 52 fingerprints found in map.
WARNING 2025-04-24 13:00:30 CrosscheckFingerprints Some samples in first column in the SECOND_INPUT_SAMPLE_MAP were not present as samples in fingerprinted file: [NotThere].
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:30 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:30 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting12072830403698673131test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:30 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:30 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:30 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:30 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint14467713583919176379.vcf --INPUT /tmp/fingerprint602062117778355363.vcf --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --SECOND_INPUT_SAMPLE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892_to_NA12891.txt --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting1802520905820876940test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:30 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:30 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
WARNING 2025-04-24 13:00:30 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:30 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:30 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint602062117778355363.vcf --INPUT_SAMPLE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892_to_NA12891.txt --SECOND_INPUT /tmp/fingerprint8526523117034821907.vcf --SECOND_INPUT_SAMPLE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892_to_NA12891.txt --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting2732030298738487654test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:30 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:30 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 1 fingerprints found in map.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:30 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:30 EDT 2025] CrosscheckFingerprints --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --INPUT_SAMPLE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892_to_NA12891.txt --SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting7773323534255172583test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:30 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:30 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam7073376866595693065.bam)
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 26 fingerprints found in map.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:30 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:30 EDT 2025] CrosscheckFingerprints --INPUT /tmp/fingerprint8888332551852945861.vcf --SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam --SECOND_INPUT_SAMPLE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892_to_NA12891.txt --CROSSCHECK_MODE CHECK_ALL_OTHERS --OUTPUT /tmp/Fingerprinting13482509659919305141test.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY SAMPLE --REQUIRE_INDEX_FILES false --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:30 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:00:30 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Fingerprinting 1 INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 2 fingerprints found in map.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam2799039651907318051.bam)
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 27 fingerprints found in map.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:30 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824