Class picard.fingerprint.CalculateFingerprintMetricsTest

all > picard.fingerprint > CalculateFingerprintMetricsTest
5

tests
0

failures
0

ignored
0.406s

duration
100%

successful

Tests

Test Duration Result
testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf) 0.064s passed
testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) 0.212s passed
testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) 0.097s passed
testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf) 0.018s passed
testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf) 0.015s passed

Standard error

[Thu Apr 24 13:00:14 EDT 2025] CalculateFingerprintMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.g.vcf --OUTPUT /tmp/testFingerprintMetric4045737086257672649fingerprint_metric --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --CALCULATE_BY READGROUP --GENOTYPE_LOD_THRESHOLD 3.0 --NUMBER_OF_SAMPLING 100 --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 13:00:14 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.
INFO	2025-04-24 13:00:14	FingerprintChecker	Processed files. 1 fingerprints found in map.
[Thu Apr 24 13:00:14 EDT 2025] picard.fingerprint.CalculateFingerprintMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:14 EDT 2025] CalculateFingerprintMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam --OUTPUT /tmp/testFingerprintMetric9508743428333276441fingerprint_metric --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --CALCULATE_BY READGROUP --GENOTYPE_LOD_THRESHOLD 3.0 --NUMBER_OF_SAMPLING 100 --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 13:00:14 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	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	FingerprintChecker	Processed files. 27 fingerprints found in map.
[Thu Apr 24 13:00:14 EDT 2025] picard.fingerprint.CalculateFingerprintMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:14 EDT 2025] CalculateFingerprintMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam --OUTPUT /tmp/testFingerprintMetric11316070654338722301fingerprint_metric --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --CALCULATE_BY READGROUP --GENOTYPE_LOD_THRESHOLD 3.0 --NUMBER_OF_SAMPLING 100 --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 13:00:14 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	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 13:00:14	FingerprintChecker	Processed files. 25 fingerprints found in map.
[Thu Apr 24 13:00:14 EDT 2025] picard.fingerprint.CalculateFingerprintMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:14 EDT 2025] CalculateFingerprintMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891.fp.vcf --OUTPUT /tmp/testFingerprintMetric4909720492675733673fingerprint_metric --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --CALCULATE_BY READGROUP --GENOTYPE_LOD_THRESHOLD 3.0 --NUMBER_OF_SAMPLING 100 --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 13:00:14 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.
INFO	2025-04-24 13:00:14	FingerprintChecker	Processed files. 1 fingerprints found in map.
[Thu Apr 24 13:00:14 EDT 2025] picard.fingerprint.CalculateFingerprintMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:14 EDT 2025] CalculateFingerprintMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12892.fp.vcf --OUTPUT /tmp/testFingerprintMetric12589610374147239714fingerprint_metric --HAPLOTYPE_MAP /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --CALCULATE_BY READGROUP --GENOTYPE_LOD_THRESHOLD 3.0 --NUMBER_OF_SAMPLING 100 --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 13:00:14 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	FingerprintChecker	Processed files. 1 fingerprints found in map.
[Thu Apr 24 13:00:14 EDT 2025] picard.fingerprint.CalculateFingerprintMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824