Class picard.fingerprint.FingerprintCheckerTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testCanHandleDeepData[0](picard.fingerprint.HaplotypeProbabilitiesFromSequence@1674b254, 10) | 0.002s | passed |
| testCanHandleDeepData[10](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@15bd8dff, 100) | 0s | passed |
| testCanHandleDeepData[11](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@15bd8dff, 500) | 0.001s | passed |
| testCanHandleDeepData[12](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@15bd8dff, 1000) | 0.002s | passed |
| testCanHandleDeepData[13](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@15bd8dff, 5000) | 0.005s | passed |
| testCanHandleDeepData[14](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@15bd8dff, 10000) | 0.010s | passed |
| testCanHandleDeepData[15](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@15bd8dff, 50000) | 0.040s | passed |
| testCanHandleDeepData[1](picard.fingerprint.HaplotypeProbabilitiesFromSequence@1674b254, 50) | 0.001s | passed |
| testCanHandleDeepData[2](picard.fingerprint.HaplotypeProbabilitiesFromSequence@1674b254, 100) | 0.001s | passed |
| testCanHandleDeepData[3](picard.fingerprint.HaplotypeProbabilitiesFromSequence@1674b254, 500) | 0.003s | passed |
| testCanHandleDeepData[4](picard.fingerprint.HaplotypeProbabilitiesFromSequence@1674b254, 1000) | 0.004s | passed |
| testCanHandleDeepData[5](picard.fingerprint.HaplotypeProbabilitiesFromSequence@1674b254, 5000) | 0.017s | passed |
| testCanHandleDeepData[6](picard.fingerprint.HaplotypeProbabilitiesFromSequence@1674b254, 10000) | 0.027s | passed |
| testCanHandleDeepData[7](picard.fingerprint.HaplotypeProbabilitiesFromSequence@1674b254, 50000) | 0.067s | passed |
| testCanHandleDeepData[8](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@15bd8dff, 10) | 0s | passed |
| testCanHandleDeepData[9](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@15bd8dff, 50) | 0.001s | passed |
| testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false) | 0.039s | passed |
| testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true) | 0.039s | passed |
| testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true) | 0.073s | passed |
| testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true) | 0.058s | passed |
| testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true) | 0.059s | passed |
| testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true) | 0.060s | passed |
| testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true) | 0.059s | passed |
| testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false) | 0.064s | passed |
| testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false) | 0.059s | passed |
| testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false) | 0.058s | passed |
| testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false) | 0.059s | passed |
| testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false) | 0.059s | passed |
| testCheckFingerprintsVcf[0](testdata/picard/fingerprint/NA12891.vcf, testdata/picard/fingerprint/NA12891.fp.vcf, NA12891, NA12891, -1.048021, -2.053484, 1.005462) | 0.033s | passed |
| testCheckFingerprintsVcf[1](testdata/picard/fingerprint/NA12891.vcf, testdata/picard/fingerprint/NA12891.g.vcf, NA12891, NA12891, -1.034969, -2.048616, 1.013647) | 0.028s | passed |
| testCheckFingerprintsVcf[2](testdata/picard/fingerprint/NA12892.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, NA12892, NA12892, -1.105025, -2.16616, 1.061135) | 0.017s | passed |
| testCheckFingerprintsVcf[3](testdata/picard/fingerprint/NA12892.vcf, testdata/picard/fingerprint/NA12892.g.vcf, NA12892, NA12892, -1.091976, -2.161961, 1.069985) | 0.018s | passed |
| testCheckFingerprintsVcf[4](testdata/picard/fingerprint/NA12891.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, NA12891, NA12892, -7.02477, -2.109822, -4.914948) | 0.015s | passed |
| testCheckFingerprintsVcf[5](testdata/picard/fingerprint/NA12891.vcf, testdata/picard/fingerprint/NA12892.g.vcf, NA12891, NA12892, -7.981971, -2.105623, -5.876347) | 0.016s | passed |
| testCheckFingerprintsVcf[6](testdata/picard/fingerprint/NA12892.vcf, testdata/picard/fingerprint/NA12891.fp.vcf, NA12892, NA12891, -7.02477, -2.109822, -4.914948) | 0.014s | passed |
| testCheckFingerprintsVcf[7](testdata/picard/fingerprint/NA12892.vcf, testdata/picard/fingerprint/NA12891.g.vcf, NA12892, NA12891, -7.924964, -2.104955, -5.820009) | 0.016s | passed |
| testCheckFingerprintsVcf[8](testdata/picard/fingerprint/emptyNA12892.vcf, testdata/picard/fingerprint/NA12891.g.vcf, NA12892, NA12891, 0, 0, 0) | 0.016s | passed |
| testFingerprintSwapEqual[0](testdata/picard/fingerprint/NA12891.vcf, testdata/picard/fingerprint/NA12891.fp.vcf, NA12891, NA12891, -1.048021, -2.053484, 1.005462) | 0.002s | passed |
| testFingerprintSwapEqual[1](testdata/picard/fingerprint/NA12891.vcf, testdata/picard/fingerprint/NA12891.g.vcf, NA12891, NA12891, -1.034969, -2.048616, 1.013647) | 0.002s | passed |
| testFingerprintSwapEqual[2](testdata/picard/fingerprint/NA12892.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, NA12892, NA12892, -1.105025, -2.16616, 1.061135) | 0.002s | passed |
| testFingerprintSwapEqual[3](testdata/picard/fingerprint/NA12892.vcf, testdata/picard/fingerprint/NA12892.g.vcf, NA12892, NA12892, -1.091976, -2.161961, 1.069985) | 0.002s | passed |
| testFingerprintSwapEqual[4](testdata/picard/fingerprint/NA12891.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, NA12891, NA12892, -7.02477, -2.109822, -4.914948) | 0.002s | passed |
| testFingerprintSwapEqual[5](testdata/picard/fingerprint/NA12891.vcf, testdata/picard/fingerprint/NA12892.g.vcf, NA12891, NA12892, -7.981971, -2.105623, -5.876347) | 0.041s | passed |
| testFingerprintSwapEqual[6](testdata/picard/fingerprint/NA12892.vcf, testdata/picard/fingerprint/NA12891.fp.vcf, NA12892, NA12891, -7.02477, -2.109822, -4.914948) | 0.002s | passed |
| testFingerprintSwapEqual[7](testdata/picard/fingerprint/NA12892.vcf, testdata/picard/fingerprint/NA12891.g.vcf, NA12892, NA12891, -7.924964, -2.104955, -5.820009) | 0.003s | passed |
| testFingerprintSwapEqual[8](testdata/picard/fingerprint/emptyNA12892.vcf, testdata/picard/fingerprint/NA12891.g.vcf, NA12892, NA12891, 0, 0, 0) | 0.002s | passed |
| testFingerprintVcf[0](testdata/picard/fingerprint/NA12891.vcf, testdata/picard/fingerprint/NA12891.fp.vcf, NA12891, NA12891, -1.048021, -2.053484, 1.005462) | 0.002s | passed |
| testFingerprintVcf[1](testdata/picard/fingerprint/NA12891.vcf, testdata/picard/fingerprint/NA12891.g.vcf, NA12891, NA12891, -1.034969, -2.048616, 1.013647) | 0.001s | passed |
| testFingerprintVcf[2](testdata/picard/fingerprint/NA12892.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, NA12892, NA12892, -1.105025, -2.16616, 1.061135) | 0.001s | passed |
| testFingerprintVcf[3](testdata/picard/fingerprint/NA12892.vcf, testdata/picard/fingerprint/NA12892.g.vcf, NA12892, NA12892, -1.091976, -2.161961, 1.069985) | 0.002s | passed |
| testFingerprintVcf[4](testdata/picard/fingerprint/NA12891.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, NA12891, NA12892, -7.02477, -2.109822, -4.914948) | 0.001s | passed |
| testFingerprintVcf[5](testdata/picard/fingerprint/NA12891.vcf, testdata/picard/fingerprint/NA12892.g.vcf, NA12891, NA12892, -7.981971, -2.105623, -5.876347) | 0.001s | passed |
| testFingerprintVcf[6](testdata/picard/fingerprint/NA12892.vcf, testdata/picard/fingerprint/NA12891.fp.vcf, NA12892, NA12891, -7.02477, -2.109822, -4.914948) | 0.001s | passed |
| testFingerprintVcf[7](testdata/picard/fingerprint/NA12892.vcf, testdata/picard/fingerprint/NA12891.g.vcf, NA12892, NA12891, -7.924964, -2.104955, -5.820009) | 0.001s | passed |
| testFingerprintVcf[8](testdata/picard/fingerprint/emptyNA12892.vcf, testdata/picard/fingerprint/NA12891.g.vcf, NA12892, NA12891, 0, 0, 0) | 0.001s | passed |
| testMatchResults[0](0.025) | 0s | passed |
| testMatchResults[10](0.275) | 0s | passed |
| testMatchResults[11](0.3) | 0s | passed |
| testMatchResults[12](0.325) | 0s | passed |
| testMatchResults[13](0.35) | 0s | passed |
| testMatchResults[14](0.375) | 0s | passed |
| testMatchResults[15](0.4) | 0s | passed |
| testMatchResults[16](0.425) | 0s | passed |
| testMatchResults[17](0.45) | 0s | passed |
| testMatchResults[18](0.475) | 0s | passed |
| testMatchResults[1](0.05) | 0s | passed |
| testMatchResults[2](0.075) | 0s | passed |
| testMatchResults[3](0.1) | 0s | passed |
| testMatchResults[4](0.125) | 0s | passed |
| testMatchResults[5](0.15) | 0s | passed |
| testMatchResults[6](0.175) | 0s | passed |
| testMatchResults[7](0.2) | 0s | passed |
| testMatchResults[8](0.225) | 0.001s | passed |
| testMatchResults[9](0.25) | 0s | passed |
| testMergeFingerprintIsSafe[0](picard.fingerprint.HaplotypeProbabilitiesFromGenotype@211f19e7, picard.fingerprint.HaplotypeProbabilitiesFromGenotype@41570983) | 0s | passed |
| testMergeFingerprintIsSafe[1](picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor@278ccad6, picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor@7e052fe1) | 0s | passed |
| testMergeFingerprintIsSafe[2](picard.fingerprint.HaplotypeProbabilitiesFromSequence@26fee400, picard.fingerprint.HaplotypeProbabilitiesFromSequence@67e55073) | 0s | passed |
| testMergeFingerprintIsSafe[3](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@e440751, picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@5fcb3c7d) | 0s | passed |
| testMergeHaplotypeProbabilitiesIsSafe[0](picard.fingerprint.HaplotypeProbabilitiesFromGenotype@62529063, picard.fingerprint.HaplotypeProbabilitiesFromGenotype@4c027df7) | 0s | passed |
| testMergeHaplotypeProbabilitiesIsSafe[1](picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor@5c13c9c5, picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor@2ab48bac) | 0s | passed |
| testMergeHaplotypeProbabilitiesIsSafe[2](picard.fingerprint.HaplotypeProbabilitiesFromSequence@5bc23ace, picard.fingerprint.HaplotypeProbabilitiesFromSequence@19dd9d92) | 0s | passed |
| testMergeHaplotypeProbabilitiesIsSafe[3](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@574a5837, picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@1d941c5a) | 0s | passed |
| testMergeIsSafeFromSequence | 0.116s | passed |
| testMergeIsSafeFromVCF | 0.007s | passed |
| testQueryableSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, false) | 0.002s | passed |
| testQueryableSam[1](/tmp/NA12891.over.fingerprints.r1.sam253450355820126963.bam, true) | 0.002s | passed |
| testQueryableVcf[0](testdata/picard/fingerprint/NA12891.fp.vcf, false) | 0.001s | passed |
| testQueryableVcf[1](testdata/picard/fingerprint/NA12891.vcf, false) | 0.001s | passed |
| testQueryableVcf[2](/tmp/fingerprintcheckertest.tmp.4809573414124188024.vcf, true) | 0.001s | passed |
| testQueryableVcf[3](/tmp/fingerprintcheckertest.tmp.12689552888302170064.vcf.gz, true) | 0.002s | passed |
| testQueryable[0](testdata/picard/fingerprint/NA12891.fp.vcf, false) | 0.001s | passed |
| testQueryable[1](testdata/picard/fingerprint/NA12891.vcf, false) | 0.001s | passed |
| testQueryable[2](/tmp/fingerprintcheckertest.tmp.8704285419741049135.vcf, true) | 0.001s | passed |
| testQueryable[3](/tmp/fingerprintcheckertest.tmp.2833155439483364767.vcf.gz, true) | 0.002s | passed |
| testTerminateOnBadFile[0](NA12891.over.fingerprints.r1.sam, true) | 0.031s | passed |
| testTerminateOnBadFile[1](aligned_queryname_sorted.sam, false) | 0.003s | passed |
| testTerminateOnBadFile[2](aligned_unsorted.sam, false) | 0.016s | passed |
| testWriteFingerprint | 0.006s | passed |
Standard error
[Thu Apr 24 13:00:32 EDT 2025] CrosscheckFingerprints --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --EXPECT_ALL_GROUPS_TO_MATCH true --VALIDATION_STRINGENCY STRICT --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 --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 --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 13:00:32 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 13:00:32 CrosscheckFingerprints Fingerprinting 2 INPUT files. WARNING 2025-04-24 13:00:32 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) WARNING 2025-04-24 13:00:32 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam) ERROR 2025-04-24 13:00:32 FingerprintChecker Found read with no readgroup: HK3T5CCXX160204:8:1214:19390:8745 in file: /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam [Thu Apr 24 13:00:32 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 13:00:32 EDT 2025] CrosscheckFingerprints --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_BY FILE --EXPECT_ALL_GROUPS_TO_MATCH true --VALIDATION_STRINGENCY STRICT --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 --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 --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 13:00:32 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 13:00:32 CrosscheckFingerprints Fingerprinting 2 INPUT files. WARNING 2025-04-24 13:00:32 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.sam) WARNING 2025-04-24 13:00:32 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam) ERROR 2025-04-24 13:00:32 FingerprintChecker Found read with no readgroup: HK3T5CCXX160204:8:1214:19390:8745 in file: /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam [Thu Apr 24 13:00:32 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 13:00:32 EDT 2025] CrosscheckFingerprints --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam --OUTPUT /tmp/crosscheck1349042978724960926.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 --EXPECT_ALL_GROUPS_TO_MATCH true --VALIDATION_STRINGENCY SILENT --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 --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 --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 13:00:32 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 13:00:32 CrosscheckFingerprints Fingerprinting 2 INPUT files. WARNING 2025-04-24 13:00:32 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.sam) WARNING 2025-04-24 13:00:33 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) INFO 2025-04-24 13:00:33 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2025-04-24 13:00:33 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2025-04-24 13:00:33 CrosscheckFingerprints All FILEs are related as expected. [Thu Apr 24 13:00:33 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:00:33 EDT 2025] CrosscheckFingerprints --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam --OUTPUT /tmp/crosscheck10445748977420087422.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 --EXPECT_ALL_GROUPS_TO_MATCH true --VALIDATION_STRINGENCY SILENT --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 --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 --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 13:00:33 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 13:00:33 CrosscheckFingerprints Fingerprinting 2 INPUT files. WARNING 2025-04-24 13:00:33 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) WARNING 2025-04-24 13:00:33 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 13:00:33 FingerprintChecker Processed files. 51 fingerprints found in map. INFO 2025-04-24 13:00:33 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2025-04-24 13:00:33 CrosscheckFingerprints All FILEs are related as expected. [Thu Apr 24 13:00:33 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:00:33 EDT 2025] CrosscheckFingerprints --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam --OUTPUT /tmp/crosscheck15945362363950415177.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 --EXPECT_ALL_GROUPS_TO_MATCH true --VALIDATION_STRINGENCY SILENT --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 --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 --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 13:00:33 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 13:00:33 CrosscheckFingerprints Fingerprinting 2 INPUT files. WARNING 2025-04-24 13:00:33 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) WARNING 2025-04-24 13:00:33 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) INFO 2025-04-24 13:00:33 FingerprintChecker Processed files. 51 fingerprints found in map. INFO 2025-04-24 13:00:33 CrosscheckFingerprints Cross-checking all FILE against each other WARNING 2025-04-24 13:00:33 CrosscheckFingerprints 2 FILEs did not relate as expected. [Thu Apr 24 13:00:33 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 13:00:33 EDT 2025] CrosscheckFingerprints --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam --OUTPUT /tmp/crosscheck4870061505470514102.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 --EXPECT_ALL_GROUPS_TO_MATCH true --VALIDATION_STRINGENCY SILENT --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 --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 --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 13:00:33 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 13:00:33 CrosscheckFingerprints Fingerprinting 2 INPUT files. WARNING 2025-04-24 13:00:33 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.sam) WARNING 2025-04-24 13:00:33 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam) INFO 2025-04-24 13:00:33 FingerprintChecker Processed files. 55 fingerprints found in map. INFO 2025-04-24 13:00:33 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2025-04-24 13:00:33 CrosscheckFingerprints All FILEs are related as expected. [Thu Apr 24 13:00:33 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:00:33 EDT 2025] CrosscheckFingerprints --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam --OUTPUT /tmp/crosscheck2090229573457075432.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 --EXPECT_ALL_GROUPS_TO_MATCH true --VALIDATION_STRINGENCY SILENT --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 --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 --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 13:00:33 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 13:00:33 CrosscheckFingerprints Fingerprinting 2 INPUT files. WARNING 2025-04-24 13:00:33 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) WARNING 2025-04-24 13:00:33 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam) INFO 2025-04-24 13:00:33 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2025-04-24 13:00:33 CrosscheckFingerprints Cross-checking all FILE against each other WARNING 2025-04-24 13:00:33 CrosscheckFingerprints 2 FILEs did not relate as expected. [Thu Apr 24 13:00:33 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 13:00:33 EDT 2025] CrosscheckFingerprints --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam --OUTPUT /tmp/crosscheck16049996684063958681.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 --EXPECT_ALL_GROUPS_TO_MATCH true --VALIDATION_STRINGENCY LENIENT --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 --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 --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 13:00:33 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 13:00:33 CrosscheckFingerprints Fingerprinting 2 INPUT files. WARNING 2025-04-24 13:00:33 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 13:00:33 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) INFO 2025-04-24 13:00:33 FingerprintChecker Processed files. 26 fingerprints found in map. INFO 2025-04-24 13:00:33 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2025-04-24 13:00:33 CrosscheckFingerprints All FILEs are related as expected. [Thu Apr 24 13:00:33 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:00:33 EDT 2025] CrosscheckFingerprints --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam --OUTPUT /tmp/crosscheck9777646467904255576.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 --EXPECT_ALL_GROUPS_TO_MATCH true --VALIDATION_STRINGENCY LENIENT --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 --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 --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 13:00:33 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 13:00:33 CrosscheckFingerprints Fingerprinting 2 INPUT files. WARNING 2025-04-24 13:00:33 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) WARNING 2025-04-24 13:00:33 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 13:00:33 FingerprintChecker Processed files. 26 fingerprints found in map. INFO 2025-04-24 13:00:33 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2025-04-24 13:00:33 CrosscheckFingerprints All FILEs are related as expected. [Thu Apr 24 13:00:33 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:00:33 EDT 2025] CrosscheckFingerprints --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam --OUTPUT /tmp/crosscheck17189363160437080957.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 --EXPECT_ALL_GROUPS_TO_MATCH true --VALIDATION_STRINGENCY LENIENT --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 --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 --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 13:00:33 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 13:00:33 CrosscheckFingerprints Fingerprinting 2 INPUT files. WARNING 2025-04-24 13:00:33 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) WARNING 2025-04-24 13:00:33 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) INFO 2025-04-24 13:00:33 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2025-04-24 13:00:33 CrosscheckFingerprints Cross-checking all FILE against each other WARNING 2025-04-24 13:00:33 CrosscheckFingerprints 2 FILEs did not relate as expected. [Thu Apr 24 13:00:33 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 13:00:33 EDT 2025] CrosscheckFingerprints --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam --OUTPUT /tmp/crosscheck3205081307420688832.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 --EXPECT_ALL_GROUPS_TO_MATCH true --VALIDATION_STRINGENCY LENIENT --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 --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 --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 13:00:33 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 13:00:33 CrosscheckFingerprints Fingerprinting 2 INPUT files. WARNING 2025-04-24 13:00:33 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 13:00:33 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam) WARNING 2025-04-24 13:00:33 FingerprintChecker Found read with no readgroup: HK3T5CCXX160204:8:1214:19390:8745 in file: /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam WARNING 2025-04-24 13:00:33 FingerprintChecker further messages from this file will be suppressed INFO 2025-04-24 13:00:33 FingerprintChecker Processed files. 54 fingerprints found in map. INFO 2025-04-24 13:00:33 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2025-04-24 13:00:33 CrosscheckFingerprints All FILEs are related as expected. [Thu Apr 24 13:00:33 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:00:33 EDT 2025] CrosscheckFingerprints --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam --OUTPUT /tmp/crosscheck2606961738468389267.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 --EXPECT_ALL_GROUPS_TO_MATCH true --VALIDATION_STRINGENCY LENIENT --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 --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 --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 13:00:33 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 13:00:33 CrosscheckFingerprints Fingerprinting 2 INPUT files. WARNING 2025-04-24 13:00:33 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) WARNING 2025-04-24 13:00:33 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam) WARNING 2025-04-24 13:00:33 FingerprintChecker Found read with no readgroup: HK3T5CCXX160204:8:1214:19390:8745 in file: /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam WARNING 2025-04-24 13:00:33 FingerprintChecker further messages from this file will be suppressed INFO 2025-04-24 13:00:33 FingerprintChecker Processed files. 54 fingerprints found in map. INFO 2025-04-24 13:00:33 CrosscheckFingerprints Cross-checking all FILE against each other WARNING 2025-04-24 13:00:33 CrosscheckFingerprints 2 FILEs did not relate as expected. [Thu Apr 24 13:00:33 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 WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.fp.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.g.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12892.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12892.fp.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12892.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12892.g.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12892.fp.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12892.g.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12892.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.fp.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12892.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.g.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/emptyNA12892.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.g.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12892.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12892.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12892.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12892.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/emptyNA12892.vcf going to read through it all. WARNING 2025-04-24 13:00:33 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.sam) WARNING 2025-04-24 13:00:33 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 13:00:33 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) WARNING 2025-04-24 13:00:33 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 13:00:33 FingerprintChecker Processed files. 104 fingerprints found in map. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.fp.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12892.fp.vcf going to read through it all. WARNING 2025-04-24 13:00:33 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12892.vcf going to read through it all. INFO 2025-04-24 13:00:33 FingerprintChecker Processed files. 4 fingerprints found in map. WARNING 2025-04-24 13:00:34 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.sam) INFO 2025-04-24 13:00:34 FingerprintChecker Processed files. 27 fingerprints found in map. WARNING 2025-04-24 13:00:34 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/aligned_queryname_sorted.sam) WARNING 2025-04-24 13:00:34 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/aligned_unsorted.sam) WARNING 2025-04-24 13:00:34 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. WARNING 2025-04-24 13:00:34 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/testSample_small.vcf going to read through it all.