Class picard.fingerprint.ClusterCrosscheckMetricsTest

[Thu Apr 24 13:00:15 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/NA12892.over.fingerprints.r1.sam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam --OUTPUT /tmp/Fingerprinting10377161184051016283NA1291_and_NA12892.RG.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --CROSSCHECK_BY FILE --EXPECT_ALL_GROUPS_TO_MATCH false --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 --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	Fingerprinting 4 INPUT files.
WARNING	2025-04-24 13:00:15	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 13:00:15	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 13:00:15	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 13:00:15	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 13:00:15	FingerprintChecker	Processed files. 104 fingerprints found in map.
INFO	2025-04-24 13:00:15	CrosscheckFingerprints	Cross-checking all FILE against each other
INFO	2025-04-24 13:00:15	CrosscheckFingerprints	All FILEs are related as expected.
[Thu Apr 24 13:00:15 EDT 2025] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:15 EDT 2025] ClusterCrosscheckMetrics --INPUT /tmp/Fingerprinting10377161184051016283NA1291_and_NA12892.RG.crosscheck_metrics --OUTPUT /tmp/Fingerprinting14078873324151827428NA1291_and_NA12892.RG.clustered_crosscheck_metrics --LOD_THRESHOLD 1.5 --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
[Thu Apr 24 13:00:15 EDT 2025] picard.fingerprint.ClusterCrosscheckMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824