Class picard.analysis.CollectWgsMetricsFromSampledSitesTest
Tests
| Test |
Duration |
Result |
| testContiguousIntervals |
1.643s |
passed |
| testLargeIntervals |
2.721s |
passed |
| testOnePos |
1.358s |
passed |
Standard error
[Tue Aug 16 04:11:29 CDT 2016] picard.analysis.CollectWgsMetricsFromSampledSites INTERVALS=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/contiguous.interval_list INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/forMetrics.sam OUTPUT=/tmp/test3527666799819992360.wgs_metrics REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta SAMPLE_SIZE=1000 MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false 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 04:11:29 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
INFO 2016-08-16 04:11:29 TheoreticalSensitivity Creating Roulette Wheel
INFO 2016-08-16 04:11:29 TheoreticalSensitivity Calculating quality sums from quality sampler
INFO 2016-08-16 04:11:29 TheoreticalSensitivity 0 sampling iterations completed
INFO 2016-08-16 04:11:30 TheoreticalSensitivity Calculating theoretical het sensitivity
[Tue Aug 16 04:11:30 CDT 2016] picard.analysis.CollectWgsMetricsFromSampledSites done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=1830289408
[Tue Aug 16 04:11:30 CDT 2016] picard.analysis.CollectWgsMetricsFromSampledSites INTERVALS=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/largeIntervals.interval_list INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/forMetrics.sam OUTPUT=/tmp/test9099983861611018489.wgs_metrics REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta SAMPLE_SIZE=1000 MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false 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 04:11:30 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
INFO 2016-08-16 04:11:30 TheoreticalSensitivity Creating Roulette Wheel
INFO 2016-08-16 04:11:30 TheoreticalSensitivity Calculating quality sums from quality sampler
INFO 2016-08-16 04:11:30 TheoreticalSensitivity 0 sampling iterations completed
INFO 2016-08-16 04:11:32 TheoreticalSensitivity Calculating theoretical het sensitivity
[Tue Aug 16 04:11:32 CDT 2016] picard.analysis.CollectWgsMetricsFromSampledSites done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1830289408
[Tue Aug 16 04:11:32 CDT 2016] picard.analysis.CollectWgsMetrics INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/forMetrics.sam OUTPUT=/tmp/collectWgsMetrics.test5511618241394110674.wgs_metrics REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta SAMPLE_SIZE=1000 INTERVALS=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/largeIntervals.interval_list MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false 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 04:11:32 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
INFO 2016-08-16 04:11:32 TheoreticalSensitivity Creating Roulette Wheel
INFO 2016-08-16 04:11:32 TheoreticalSensitivity Calculating quality sums from quality sampler
INFO 2016-08-16 04:11:32 TheoreticalSensitivity 0 sampling iterations completed
INFO 2016-08-16 04:11:33 TheoreticalSensitivity Calculating theoretical het sensitivity
[Tue Aug 16 04:11:33 CDT 2016] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1830289408
[Tue Aug 16 04:11:33 CDT 2016] picard.analysis.CollectWgsMetricsFromSampledSites INTERVALS=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/onePos.interval_list INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/forMetrics.sam OUTPUT=/tmp/test4778875262100783629.wgs_metrics REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta INCLUDE_BQ_HISTOGRAM=true SAMPLE_SIZE=1000 MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 COUNT_UNPAIRED=false 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 04:11:33 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
INFO 2016-08-16 04:11:33 TheoreticalSensitivity Creating Roulette Wheel
INFO 2016-08-16 04:11:33 TheoreticalSensitivity Calculating quality sums from quality sampler
INFO 2016-08-16 04:11:33 TheoreticalSensitivity 0 sampling iterations completed
INFO 2016-08-16 04:11:34 TheoreticalSensitivity Calculating theoretical het sensitivity
[Tue Aug 16 04:11:34 CDT 2016] picard.analysis.CollectWgsMetricsFromSampledSites done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1830289408