Class picard.analysis.CollectMultipleMetricsTest
Tests
| Test |
Duration |
Result |
| testAlignmentSummaryViaMultipleMetrics |
0.297s |
passed |
| testGcBiasMetrics |
0.627s |
passed |
| testInsertSize |
0.284s |
passed |
Standard error
[Tue Aug 16 04:11:24 CDT 2016] picard.analysis.CollectMultipleMetrics INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics5788482954998404585 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_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 04:11:24 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 04:11:24 RExecutor Executing R script via command: Rscript /tmp/script7255648938759339195.R /tmp/alignmentMetrics5788482954998404585.insert_size_metrics /tmp/alignmentMetrics5788482954998404585.insert_size_histogram.pdf summary_alignment_stats_test.sam
INFO 2016-08-16 04:11:24 ProcessExecutor null device
INFO 2016-08-16 04:11:24 ProcessExecutor 1
[Tue Aug 16 04:11:24 CDT 2016] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:24 CDT 2016] picard.analysis.CollectMultipleMetrics INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias7639143478311535827.bam OUTPUT=/tmp/test2002616239336033127 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics, CollectGcBiasMetrics] REFERENCE_SEQUENCE=testdata/picard/quality/chrM.reference.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_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 04:11:24 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 04:11:25 RExecutor Executing R script via command: Rscript /tmp/script3850528895771985924.R /tmp/test2002616239336033127.insert_size_metrics /tmp/test2002616239336033127.insert_size_histogram.pdf CollectGcBias7639143478311535827.bam
INFO 2016-08-16 04:11:25 ProcessExecutor null device
INFO 2016-08-16 04:11:25 ProcessExecutor 1
INFO 2016-08-16 04:11:25 RExecutor Executing R script via command: Rscript /tmp/script2325109185060555073.R /tmp/test2002616239336033127.gc_bias.detail_metrics /tmp/test2002616239336033127.gc_bias.summary_metrics /tmp/test2002616239336033127.gc_bias.pdf 100
INFO 2016-08-16 04:11:25 ProcessExecutor Total clusters: 300 , Aligned reads: 600
[Tue Aug 16 04:11:25 CDT 2016] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:25 CDT 2016] picard.analysis.CollectMultipleMetrics INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/insert_size_metrics_test.sam OUTPUT=/tmp/test1145473191581527949 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_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 04:11:25 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 04:11:25 RExecutor Executing R script via command: Rscript /tmp/script713411944089554949.R /tmp/test1145473191581527949.insert_size_metrics /tmp/test1145473191581527949.insert_size_histogram.pdf insert_size_metrics_test.sam
INFO 2016-08-16 04:11:25 ProcessExecutor null device
INFO 2016-08-16 04:11:25 ProcessExecutor 1
[Tue Aug 16 04:11:25 CDT 2016] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120