Class picard.fingerprint.CheckFingerprintTest

all > picard.fingerprint > CheckFingerprintTest
28

tests
0

failures
0

ignored
0.476s

duration
100%

successful

Tests

Test Duration Result
extractObservedSampleNameExceptionTest[0](testdata/picard/fingerprint/NA12891.fp.vcf, NA12892) 0.001s passed
extractObservedSampleNameExceptionTest[1](testdata/picard/fingerprint/NA12891andNA12892.vcf, null) 0s passed
testBadData[0](/mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt) 0.010s passed
testBadData[1](/mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/noFile.vcf, /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt) 0.009s passed
testBadData[2](/mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.vcf, /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt) 0.009s passed
testBadData[3](/mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/noFile.vcf, /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt) 0.010s passed
testBaseOutput 0.018s passed
testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0) 0.054s passed
testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1) 0.016s passed
testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0) 0.052s passed
testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1) 0.016s passed
testCheckFingerprintVcf[0](/tmp/fingerprint12896690812919421909.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0) 0.017s passed
testCheckFingerprintVcf[1](/tmp/fingerprint7853817687867416534.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0) 0.016s passed
testContainsSample[0](testdata/picard/fingerprint/NA12891.fp.vcf, NA12891, true) 0.001s passed
testContainsSample[1](testdata/picard/fingerprint/NA12891.fp.vcf, NA12892, false) 0s passed
testContainsSample[2](testdata/picard/fingerprint/NA12892.fp.vcf, NA12891, false) 0.001s passed
testContainsSample[3](testdata/picard/fingerprint/NA12892.fp.vcf, NA12892, true) 0s passed
testExtractObservedSampleNameDataProvider[0](testdata/picard/fingerprint/NA12891.fp.vcf, null, NA12891) 0s passed
testExtractObservedSampleNameDataProvider[1](testdata/picard/fingerprint/NA12892.fp.vcf, null, NA12892) 0.001s passed
testExtractObservedSampleNameDataProvider[2](testdata/picard/fingerprint/NA12891andNA12892.vcf, NA12892, NA12892) 0s passed
testFPToVC 0.051s passed
testIdentifyContaminant 0.098s passed
testMismatchingAndMissing[0](/mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, [], 1) 0.019s passed
testMismatchingAndMissing[1](/mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.vcf, [EXPECTED_SAMPLE_ALIAS=TEST123], 1) 0.016s passed
testMismatchingAndMissing[2](/mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.vcf, [EXPECTED_SAMPLE_ALIAS=TEST123, EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND=0], 0) 0.014s passed
testMismatchingAndMissing[3](/mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/empty.vcf, [], 2) 0.016s passed
testMismatchingAndMissing[4](/mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/empty.vcf, [EXIT_CODE_WHEN_NO_VALID_CHECKS=0], 0) 0.015s passed
testSummaryAndDetailOutputs 0.016s passed

Standard error

[Thu Apr 24 13:00:14 EDT 2025] CheckFingerprint --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/tempCheckFPDir/void.vcf --OUTPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/tempCheckFPDir/otp.fp --GENOTYPES /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.g.vcf --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --GENOTYPE_LOD_THRESHOLD 5.0 --IGNORE_READ_GROUPS false --EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 2 --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 13:00:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 13:00:14 EDT 2025] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:14 EDT 2025] CheckFingerprint --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/noFile.vcf --OUTPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/tempCheckFPDir/otp.fp --GENOTYPES /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.g.vcf --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --GENOTYPE_LOD_THRESHOLD 5.0 --IGNORE_READ_GROUPS false --EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 2 --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 13:00:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 13:00:14 EDT 2025] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:14 EDT 2025] CheckFingerprint --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.vcf --OUTPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/tempCheckFPDir/otp.fp --GENOTYPES /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/noFile.g.vcf --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --GENOTYPE_LOD_THRESHOLD 5.0 --IGNORE_READ_GROUPS false --EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 2 --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 13:00:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 13:00:14 EDT 2025] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:14 EDT 2025] CheckFingerprint --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/noFile.vcf --OUTPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/tempCheckFPDir/otp.fp --GENOTYPES /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/noFile.g.vcf --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --GENOTYPE_LOD_THRESHOLD 5.0 --IGNORE_READ_GROUPS false --EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 2 --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 13:00:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 13:00:14 EDT 2025] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:14 EDT 2025] CheckFingerprint --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.vcf --OUTPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/tempCheckFPDir/otp.fp --GENOTYPES /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.g.vcf --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --GENOTYPE_LOD_THRESHOLD 5.0 --IGNORE_READ_GROUPS false --EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 2 --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 13:00:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
WARNING	2025-04-24 13:00:14	FingerprintChecker	Couldn't find index for file /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.g.vcf going to read through it all.
WARNING	2025-04-24 13:00:14	FingerprintChecker	Couldn't find index for file /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.vcf going to read through it all.
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: null / NA12892 vs. NA12892: LOD = 1.0699858771062327
[Thu Apr 24 13:00:14 EDT 2025] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:14 EDT 2025] CheckFingerprint --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam --SUMMARY_OUTPUT /tmp/fingerprint17809861729849992407summary_metrics --DETAIL_OUTPUT /tmp/fingerprint13317426344790564041detail_metrics --GENOTYPES /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.fp.vcf --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --IGNORE_READ_GROUPS true --GENOTYPE_LOD_THRESHOLD 5.0 --EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 2 --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 13:00:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
WARNING	2025-04-24 13:00:14	FingerprintChecker	Couldn't find index for file /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.fp.vcf going to read through it all.
WARNING	2025-04-24 13:00:14	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 13:00:14	CheckFingerprint	Read Group: null / NA12891 vs. NA12891: LOD = 1.9575410308482257
[Thu Apr 24 13:00:14 EDT 2025] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:14 EDT 2025] CheckFingerprint --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam --SUMMARY_OUTPUT /tmp/fingerprint16164829583126593050summary_metrics --DETAIL_OUTPUT /tmp/fingerprint6250736430200745577detail_metrics --GENOTYPES /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.fp.vcf --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --IGNORE_READ_GROUPS true --GENOTYPE_LOD_THRESHOLD 5.0 --EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 2 --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 13:00:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
WARNING	2025-04-24 13:00:14	CheckFingerprint	Sample NA12892 where fingerprint was expected not found in /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.fp.vcf
[Thu Apr 24 13:00:14 EDT 2025] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:14 EDT 2025] CheckFingerprint --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam --SUMMARY_OUTPUT /tmp/fingerprint15889265800731530854summary_metrics --DETAIL_OUTPUT /tmp/fingerprint5713981923039548210detail_metrics --GENOTYPES /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.fp.vcf --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --GENOTYPE_LOD_THRESHOLD 5.0 --IGNORE_READ_GROUPS false --EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 2 --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 13:00:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
WARNING	2025-04-24 13:00:14	FingerprintChecker	Couldn't find index for file /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.fp.vcf going to read through it all.
WARNING	2025-04-24 13:00:14	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 13:00:14	CheckFingerprint	Read Group: HK35NCCXX160204.1.TATCCAGG / NA12891 vs. NA12891: LOD = 0.6767828904844997
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HK35NCCXX160204.2.TATCCAGG / NA12891 vs. NA12891: LOD = -0.1777885789893492
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HTL2KCCXX160412.5.TATCCAGG-GAAGTGGA / NA12891 vs. NA12891: LOD = 0.6821768525202883
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HTL2KCCXX160412.6.TATCCAGG-GAAGTGGA / NA12891 vs. NA12891: LOD = 1.5638358662469267
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HJYN2CCXX160123.1.TATCCAGG / NA12891 vs. NA12891: LOD = 0.7515877715986727
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HK3T5CCXX160204.1.TATCCAGG / NA12891 vs. NA12891: LOD = 0.5790017814227286
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HK3T5CCXX160204.2.TATCCAGG / NA12891 vs. NA12891: LOD = 0.7368081322746325
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HK3T5CCXX160204.3.TATCCAGG / NA12891 vs. NA12891: LOD = 0.4286259057547821
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HK3T5CCXX160204.4.TATCCAGG / NA12891 vs. NA12891: LOD = 1.105755285701254
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HK3T5CCXX160204.5.TATCCAGG / NA12891 vs. NA12891: LOD = 0.21447953267151032
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HK3T5CCXX160204.6.TATCCAGG / NA12891 vs. NA12891: LOD = 0.8376997076761636
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HK3T5CCXX160204.7.TATCCAGG / NA12891 vs. NA12891: LOD = 0.8813562283192153
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HK3T5CCXX160204.8.TATCCAGG / NA12891 vs. NA12891: LOD = 0.9989888195257852
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HK35MCCXX160204.1.TATCCAGG / NA12891 vs. NA12891: LOD = 1.04405813553949
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HK35MCCXX160204.2.TATCCAGG / NA12891 vs. NA12891: LOD = 0.5893772852178616
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HK35MCCXX160204.3.TATCCAGG / NA12891 vs. NA12891: LOD = 0.4593438456798795
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HK35MCCXX160204.4.TATCCAGG / NA12891 vs. NA12891: LOD = 1.1930705126333643
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HK35MCCXX160204.5.TATCCAGG / NA12891 vs. NA12891: LOD = 0.642675010900108
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HK35MCCXX160204.6.TATCCAGG / NA12891 vs. NA12891: LOD = 0.1844134560992945
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HK35MCCXX160204.7.TATCCAGG / NA12891 vs. NA12891: LOD = 0.2934236641373207
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HK35MCCXX160204.8.TATCCAGG / NA12891 vs. NA12891: LOD = 0.3307277843999552
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HJYFJCCXX160204.4.TATCCAGG / NA12891 vs. NA12891: LOD = -0.016667966118423472
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HJYFJCCXX160204.5.TATCCAGG / NA12891 vs. NA12891: LOD = 1.4949377033063986
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HJYFJCCXX160204.6.TATCCAGG / NA12891 vs. NA12891: LOD = -0.09171156502005773
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HJYFJCCXX160204.7.TATCCAGG / NA12891 vs. NA12891: LOD = -0.09768004672552877
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HJYFJCCXX160204.8.TATCCAGG / NA12891 vs. NA12891: LOD = 0.7893729828153071
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: HM3G2CCXX160308.2.TATCCAGG / NA12891 vs. NA12891: LOD = 1.9575145012761315
[Thu Apr 24 13:00:14 EDT 2025] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:14 EDT 2025] CheckFingerprint --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam --SUMMARY_OUTPUT /tmp/fingerprint1542841939306580864summary_metrics --DETAIL_OUTPUT /tmp/fingerprint4438532492869570313detail_metrics --GENOTYPES /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.fp.vcf --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --GENOTYPE_LOD_THRESHOLD 5.0 --IGNORE_READ_GROUPS false --EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 2 --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 13:00:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
WARNING	2025-04-24 13:00:14	CheckFingerprint	Sample NA12892 where fingerprint was expected not found in /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.fp.vcf
[Thu Apr 24 13:00:14 EDT 2025] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:14 EDT 2025] CheckFingerprint --INPUT /tmp/fingerprint12896690812919421909.vcf --SUMMARY_OUTPUT /tmp/fingerprint18218958729651317240summary_metrics --DETAIL_OUTPUT /tmp/fingerprint6081969680896803954detail_metrics --GENOTYPES /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.fp.vcf --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --GENOTYPE_LOD_THRESHOLD 5.0 --IGNORE_READ_GROUPS false --EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 2 --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 13:00:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
WARNING	2025-04-24 13:00:14	FingerprintChecker	Couldn't find index for file /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.fp.vcf going to read through it all.
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: null / NA12892 vs. NA12892: LOD = -4.9149484155816
[Thu Apr 24 13:00:14 EDT 2025] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:14 EDT 2025] CheckFingerprint --INPUT /tmp/fingerprint7853817687867416534.vcf --SUMMARY_OUTPUT /tmp/fingerprint9816914551010848896summary_metrics --DETAIL_OUTPUT /tmp/fingerprint18357806176755602527detail_metrics --GENOTYPES /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.fp.vcf --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --GENOTYPE_LOD_THRESHOLD 5.0 --IGNORE_READ_GROUPS false --EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 2 --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 13:00:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
WARNING	2025-04-24 13:00:14	FingerprintChecker	Couldn't find index for file /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.fp.vcf going to read through it all.
INFO	2025-04-24 13:00:14	CheckFingerprint	Read Group: null / NA12892 vs. NA12892: LOD = 1.06113519110639
[Thu Apr 24 13:00:14 EDT 2025] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
WARNING	2025-04-24 13:00:14	FingerprintChecker	Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.shifted.for.crams.r1.sam)
INFO	2025-04-24 13:00:15	FingerprintChecker	Processed files. 1 fingerprints found in map.
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.shifted.for.crams.r1.sam)
INFO	2025-04-24 13:00:15	FingerprintChecker	Processed files. 27 fingerprints found in map.
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.shifted.for.crams.r1.sam)
INFO	2025-04-24 13:00:15	FingerprintChecker	Processed files. 25 fingerprints found in map.
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/NA128791_in_NA12892.25_PCT.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)
INFO	2025-04-24 13:00:15	FingerprintChecker	Processed files. 26 fingerprints found in map.
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. 26 fingerprints found in map.
[Thu Apr 24 13:00:15 EDT 2025] CheckFingerprint --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam --OUTPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/tempCheckFPDir/otp.fp --GENOTYPES /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.g.vcf --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --GENOTYPE_LOD_THRESHOLD 5.0 --IGNORE_READ_GROUPS false --EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 2 --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
WARNING	2025-04-24 13:00:15	CheckFingerprint	Sample NA12891 where fingerprint was expected not found in /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.g.vcf
[Thu Apr 24 13:00:15 EDT 2025] picard.fingerprint.CheckFingerprint 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] CheckFingerprint --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.vcf --OUTPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/tempCheckFPDir/otp.fp --GENOTYPES /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.g.vcf --EXPECTED_SAMPLE_ALIAS TEST123 --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --GENOTYPE_LOD_THRESHOLD 5.0 --IGNORE_READ_GROUPS false --EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 2 --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
WARNING	2025-04-24 13:00:15	CheckFingerprint	Sample TEST123 where fingerprint was expected not found in /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.g.vcf
[Thu Apr 24 13:00:15 EDT 2025] picard.fingerprint.CheckFingerprint 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] CheckFingerprint --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.vcf --OUTPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/tempCheckFPDir/otp.fp --GENOTYPES /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.g.vcf --EXPECTED_SAMPLE_ALIAS TEST123 --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND 0 --GENOTYPE_LOD_THRESHOLD 5.0 --IGNORE_READ_GROUPS false --EXIT_CODE_WHEN_NO_VALID_CHECKS 2 --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
WARNING	2025-04-24 13:00:15	CheckFingerprint	Sample TEST123 where fingerprint was expected not found in /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.g.vcf
[Thu Apr 24 13:00:15 EDT 2025] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:15 EDT 2025] CheckFingerprint --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/empty.vcf --OUTPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/tempCheckFPDir/otp.fp --GENOTYPES /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.g.vcf --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --GENOTYPE_LOD_THRESHOLD 5.0 --IGNORE_READ_GROUPS false --EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 2 --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
WARNING	2025-04-24 13:00:15	FingerprintChecker	Couldn't find index for file /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.g.vcf going to read through it all.
WARNING	2025-04-24 13:00:15	FingerprintChecker	Couldn't find index for file /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/empty.vcf going to read through it all.
INFO	2025-04-24 13:00:15	CheckFingerprint	Read Group: null / NA12892 vs. NA12892: LOD = 0.0
ERROR	2025-04-24 13:00:15	CheckFingerprint	No non-zero results found. This is likely an error. Probable cause: EXPECTED_SAMPLE (if provided) or the sample name from INPUT (if EXPECTED_SAMPLE isn't provided)isn't a sample in GENOTYPES file.
[Thu Apr 24 13:00:15 EDT 2025] picard.fingerprint.CheckFingerprint 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] CheckFingerprint --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/empty.vcf --OUTPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/tempCheckFPDir/otp.fp --GENOTYPES /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.g.vcf --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --EXIT_CODE_WHEN_NO_VALID_CHECKS 0 --GENOTYPE_LOD_THRESHOLD 5.0 --IGNORE_READ_GROUPS false --EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND 1 --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
WARNING	2025-04-24 13:00:15	FingerprintChecker	Couldn't find index for file /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.g.vcf going to read through it all.
WARNING	2025-04-24 13:00:15	FingerprintChecker	Couldn't find index for file /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/empty.vcf going to read through it all.
INFO	2025-04-24 13:00:15	CheckFingerprint	Read Group: null / NA12892 vs. NA12892: LOD = 0.0
ERROR	2025-04-24 13:00:15	CheckFingerprint	No non-zero results found. This is likely an error. Probable cause: EXPECTED_SAMPLE (if provided) or the sample name from INPUT (if EXPECTED_SAMPLE isn't provided)isn't a sample in GENOTYPES file.
[Thu Apr 24 13:00:15 EDT 2025] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:15 EDT 2025] CheckFingerprint --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.vcf --SUMMARY_OUTPUT testdata/picard/fingerprint/tempCheckFPDir/summary --DETAIL_OUTPUT testdata/picard/fingerprint/tempCheckFPDir/detail --GENOTYPES /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.g.vcf --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --GENOTYPE_LOD_THRESHOLD 5.0 --IGNORE_READ_GROUPS false --EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 2 --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
WARNING	2025-04-24 13:00:15	FingerprintChecker	Couldn't find index for file /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.g.vcf going to read through it all.
WARNING	2025-04-24 13:00:15	FingerprintChecker	Couldn't find index for file /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.vcf going to read through it all.
INFO	2025-04-24 13:00:15	CheckFingerprint	Read Group: null / NA12892 vs. NA12892: LOD = 1.0699858771062327
[Thu Apr 24 13:00:15 EDT 2025] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824