Class picard.analysis.artifacts.CollectSequencingArtifactMetricsTest
Tests
| Test |
Duration |
Result |
| testContext |
0.100s |
passed |
| testDbSnp |
0.042s |
passed |
| testIntervalList |
0.036s |
passed |
| testNoBqCutoff |
0.033s |
passed |
| testNoMqCutoff |
0.034s |
passed |
| testUnmappedMate |
0.030s |
passed |
Standard error
[Tue Aug 16 04:11:26 CDT 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=1 INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.7153719608862607617.tmp/with_context REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=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=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:26 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
[Tue Aug 16 04:11:26 CDT 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:26 CDT 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics DB_SNP=testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.dbsnp.vcf MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=0 INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.7153719608862607617.tmp/with_dbsnp REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=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=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:26 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
[Tue Aug 16 04:11:26 CDT 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:26 CDT 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics INTERVALS=testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.interval_list MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=0 INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.7153719608862607617.tmp/with_intervals REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=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=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:26 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
[Tue Aug 16 04:11:26 CDT 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:26 CDT 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=0 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=0 INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.7153719608862607617.tmp/no_bq_cutoff REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=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=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:26 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
[Tue Aug 16 04:11:26 CDT 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:26 CDT 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics MINIMUM_MAPPING_QUALITY=0 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=0 INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.7153719608862607617.tmp/no_mq_cutoff REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_QUALITY_SCORE=20 INCLUDE_UNPAIRED=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=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:26 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
[Tue Aug 16 04:11:26 CDT 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:26 CDT 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics MINIMUM_INSERT_SIZE=0 MAXIMUM_INSERT_SIZE=0 CONTEXT_SIZE=0 INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.7153719608862607617.tmp/unmapped_mate REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=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=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:26 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
[Tue Aug 16 04:11:26 CDT 2016] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120