Standard error
[Tue Aug 16 04:11:34 CDT 2016] picard.analysis.CollectWgsMetrics INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CollectWgsMetrics1120936304069118188.bam OUTPUT=/tmp/testWgsMetrics7123377949225201128.txt REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta COVERAGE_CAP=3 INCLUDE_BQ_HISTOGRAM=true MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 COUNT_UNPAIRED=false SAMPLE_SIZE=10000 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 04:11:34 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
WARNING 2016-08-16 04:11:34 SamLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not.
INFO 2016-08-16 04:11:34 TheoreticalSensitivity Creating Roulette Wheel
INFO 2016-08-16 04:11:34 TheoreticalSensitivity Calculating quality sums from quality sampler
INFO 2016-08-16 04:11:34 TheoreticalSensitivity 0 sampling iterations completed
INFO 2016-08-16 04:11:34 TheoreticalSensitivity 1000 sampling iterations completed
INFO 2016-08-16 04:11:34 TheoreticalSensitivity 2000 sampling iterations completed
INFO 2016-08-16 04:11:34 TheoreticalSensitivity 3000 sampling iterations completed
INFO 2016-08-16 04:11:34 TheoreticalSensitivity 4000 sampling iterations completed
INFO 2016-08-16 04:11:34 TheoreticalSensitivity 5000 sampling iterations completed
INFO 2016-08-16 04:11:34 TheoreticalSensitivity 6000 sampling iterations completed
INFO 2016-08-16 04:11:34 TheoreticalSensitivity 7000 sampling iterations completed
INFO 2016-08-16 04:11:34 TheoreticalSensitivity 8000 sampling iterations completed
INFO 2016-08-16 04:11:35 TheoreticalSensitivity 9000 sampling iterations completed
INFO 2016-08-16 04:11:35 TheoreticalSensitivity Calculating theoretical het sensitivity
[Tue Aug 16 04:11:35 CDT 2016] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1830289408
[Tue Aug 16 04:11:35 CDT 2016] picard.analysis.CollectWgsMetrics INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/forMetrics.sam OUTPUT=/tmp/test5622801981293099628.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 04:11:35 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 04:11:35 TheoreticalSensitivity Creating Roulette Wheel
INFO 2016-08-16 04:11:35 TheoreticalSensitivity Calculating quality sums from quality sampler
INFO 2016-08-16 04:11:35 TheoreticalSensitivity 0 sampling iterations completed
INFO 2016-08-16 04:11:36 TheoreticalSensitivity Calculating theoretical het sensitivity
[Tue Aug 16 04:11:36 CDT 2016] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=1830289408
[Tue Aug 16 04:11:36 CDT 2016] picard.analysis.CollectWgsMetrics INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CollectWgsMetrics9202878205286795487.bam OUTPUT=/tmp/testWgsMetrics2090396577993031957.txt REFERENCE_SEQUENCE=testdata/picard/quality/chrM.reference.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 04:11:36 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 04:11:37 TheoreticalSensitivity Creating Roulette Wheel
INFO 2016-08-16 04:11:37 TheoreticalSensitivity Calculating quality sums from quality sampler
INFO 2016-08-16 04:11:37 TheoreticalSensitivity 0 sampling iterations completed
INFO 2016-08-16 04:11:37 TheoreticalSensitivity Calculating theoretical het sensitivity
[Tue Aug 16 04:11:37 CDT 2016] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1823997952