Class picard.analysis.artifacts.CollectSequencingArtifactMetricsTest
Tests
| Test |
Duration |
Result |
| runIUPACCase |
0.014s |
passed |
| testContext |
0.036s |
passed |
| testDbSnp |
0.015s |
passed |
| testIntervalList |
0.012s |
passed |
| testLargerContext |
0.197s |
passed |
| testNoBqCutoff |
0.013s |
passed |
| testNoMqCutoff |
0.013s |
passed |
| testUnmappedMate |
0.012s |
passed |
Standard error
[Thu Apr 24 12:59:53 EDT 2025] CollectSequencingArtifactMetrics --MINIMUM_INSERT_SIZE 30 --MAXIMUM_INSERT_SIZE 30 --CONTEXT_SIZE 0 --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/testWithIUPACBases.sam --OUTPUT /tmp/artifactMetrics.tmp9219062085544579536/IUPAC --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta --MINIMUM_QUALITY_SCORE 20 --MINIMUM_MAPPING_QUALITY 30 --INCLUDE_UNPAIRED false --INCLUDE_DUPLICATES false --INCLUDE_NON_PF_READS false --TANDEM_READS false --USE_OQ true --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:53 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 12:59:53 EDT 2025] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:53 EDT 2025] CollectSequencingArtifactMetrics --MINIMUM_INSERT_SIZE 30 --MAXIMUM_INSERT_SIZE 30 --CONTEXT_SIZE 1 --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam --OUTPUT /tmp/artifactMetrics.tmp9219062085544579536/with_context --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta --MINIMUM_QUALITY_SCORE 20 --MINIMUM_MAPPING_QUALITY 30 --INCLUDE_UNPAIRED false --INCLUDE_DUPLICATES false --INCLUDE_NON_PF_READS false --TANDEM_READS false --USE_OQ true --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:53 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 12:59:53 EDT 2025] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:53 EDT 2025] CollectSequencingArtifactMetrics --DB_SNP testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.dbsnp.vcf --MINIMUM_INSERT_SIZE 30 --MAXIMUM_INSERT_SIZE 30 --CONTEXT_SIZE 0 --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam --OUTPUT /tmp/artifactMetrics.tmp9219062085544579536/with_dbsnp --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta --MINIMUM_QUALITY_SCORE 20 --MINIMUM_MAPPING_QUALITY 30 --INCLUDE_UNPAIRED false --INCLUDE_DUPLICATES false --INCLUDE_NON_PF_READS false --TANDEM_READS false --USE_OQ true --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:53 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 12:59:53 EDT 2025] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:53 EDT 2025] CollectSequencingArtifactMetrics --INTERVALS testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.interval_list --MINIMUM_INSERT_SIZE 30 --MAXIMUM_INSERT_SIZE 30 --CONTEXT_SIZE 0 --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam --OUTPUT /tmp/artifactMetrics.tmp9219062085544579536/with_intervals --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta --MINIMUM_QUALITY_SCORE 20 --MINIMUM_MAPPING_QUALITY 30 --INCLUDE_UNPAIRED false --INCLUDE_DUPLICATES false --INCLUDE_NON_PF_READS false --TANDEM_READS false --USE_OQ true --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:53 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 12:59:53 EDT 2025] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:53 EDT 2025] CollectSequencingArtifactMetrics --MINIMUM_INSERT_SIZE 30 --MAXIMUM_INSERT_SIZE 30 --CONTEXT_SIZE 2 --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam --OUTPUT /tmp/artifactMetrics.tmp9219062085544579536/with_larger_context --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta --MINIMUM_QUALITY_SCORE 20 --MINIMUM_MAPPING_QUALITY 30 --INCLUDE_UNPAIRED false --INCLUDE_DUPLICATES false --INCLUDE_NON_PF_READS false --TANDEM_READS false --USE_OQ true --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:53 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 12:59:53 EDT 2025] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:53 EDT 2025] CollectSequencingArtifactMetrics --MINIMUM_QUALITY_SCORE 0 --MINIMUM_INSERT_SIZE 30 --MAXIMUM_INSERT_SIZE 30 --CONTEXT_SIZE 0 --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam --OUTPUT /tmp/artifactMetrics.tmp9219062085544579536/no_bq_cutoff --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta --MINIMUM_MAPPING_QUALITY 30 --INCLUDE_UNPAIRED false --INCLUDE_DUPLICATES false --INCLUDE_NON_PF_READS false --TANDEM_READS false --USE_OQ true --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:53 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 12:59:53 EDT 2025] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:53 EDT 2025] CollectSequencingArtifactMetrics --MINIMUM_MAPPING_QUALITY 0 --MINIMUM_INSERT_SIZE 30 --MAXIMUM_INSERT_SIZE 30 --CONTEXT_SIZE 0 --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam --OUTPUT /tmp/artifactMetrics.tmp9219062085544579536/no_mq_cutoff --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta --MINIMUM_QUALITY_SCORE 20 --INCLUDE_UNPAIRED false --INCLUDE_DUPLICATES false --INCLUDE_NON_PF_READS false --TANDEM_READS false --USE_OQ true --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:53 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 12:59:53 EDT 2025] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:53 EDT 2025] CollectSequencingArtifactMetrics --MINIMUM_INSERT_SIZE 0 --MAXIMUM_INSERT_SIZE 0 --CONTEXT_SIZE 0 --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam --OUTPUT /tmp/artifactMetrics.tmp9219062085544579536/unmapped_mate --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta --MINIMUM_QUALITY_SCORE 20 --MINIMUM_MAPPING_QUALITY 30 --INCLUDE_UNPAIRED false --INCLUDE_DUPLICATES false --INCLUDE_NON_PF_READS false --TANDEM_READS false --USE_OQ true --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:53 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 12:59:53 EDT 2025] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824