Class picard.analysis.CollectGcBiasMetricsTest

[Tue Aug 16 04:11:18 CDT 2016] picard.analysis.CollectGcBiasMetrics CHART_OUTPUT=/tmp/test2608553140100541125.pdf SUMMARY_OUTPUT=/tmp/test1468613807220455983.gc_bias.summary_metrics SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 IS_BISULFITE_SEQUENCED=false METRIC_ACCUMULATION_LEVEL=[SAMPLE, READ_GROUP, ALL_READS] INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias3738686547354687812.bam OUTPUT=/tmp/test8086345441319508654.gc_bias.detail_metrics ASSUME_SORTED=false REFERENCE_SEQUENCE=testdata/picard/metrics/chrMNO.reference.fasta    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 04:11:18 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 04:11:18	RExecutor	Executing R script via command: Rscript /tmp/script4852204460796580274.R /tmp/test8086345441319508654.gc_bias.detail_metrics /tmp/test1468613807220455983.gc_bias.summary_metrics /tmp/test2608553140100541125.pdf 100
INFO	2016-08-16 04:11:19	ProcessExecutor	Total clusters:  300 , Aligned reads:  600Total clusters:  200 , Aligned reads:  400Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200
[Tue Aug 16 04:11:19 CDT 2016] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:19 CDT 2016] picard.analysis.CollectGcBiasMetrics CHART_OUTPUT=/tmp/test2437101689465705770.pdf SUMMARY_OUTPUT=/tmp/test8121522690437421614.gc_bias_summary_metrics SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 IS_BISULFITE_SEQUENCED=false METRIC_ACCUMULATION_LEVEL=[SAMPLE, READ_GROUP, ALL_READS] INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias3738686547354687812.bam OUTPUT=/tmp/test8000941811058579217.gc_bias_detail_metrics ASSUME_SORTED=false REFERENCE_SEQUENCE=testdata/picard/metrics/chrMNO.reference.fasta    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 04:11:19 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 04:11:19	RExecutor	Executing R script via command: Rscript /tmp/script5748696460136940244.R /tmp/test8000941811058579217.gc_bias_detail_metrics /tmp/test8121522690437421614.gc_bias_summary_metrics /tmp/test2437101689465705770.pdf 100
INFO	2016-08-16 04:11:19	ProcessExecutor	Total clusters:  300 , Aligned reads:  600Total clusters:  200 , Aligned reads:  400Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200
[Tue Aug 16 04:11:19 CDT 2016] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:19 CDT 2016] picard.analysis.CollectGcBiasMetrics CHART_OUTPUT=/tmp/test6900502563470361488.pdf SUMMARY_OUTPUT=/tmp/testAllChr7362271205019339238.gc_bias_summary_metrics SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 IS_BISULFITE_SEQUENCED=false METRIC_ACCUMULATION_LEVEL=[SAMPLE, READ_GROUP, ALL_READS] INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias8941737080081751342.bam OUTPUT=/tmp/testAllChrDetails5976179304516329124.gc_bias_detail_metrics ASSUME_SORTED=false REFERENCE_SEQUENCE=testdata/picard/metrics/chrMNO.reference.fasta    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 04:11:19 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 04:11:19	RExecutor	Executing R script via command: Rscript /tmp/script7476667056122300058.R /tmp/testAllChrDetails5976179304516329124.gc_bias_detail_metrics /tmp/testAllChr7362271205019339238.gc_bias_summary_metrics /tmp/test6900502563470361488.pdf 100
INFO	2016-08-16 04:11:19	ProcessExecutor	Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200Total clusters:  100 , Aligned reads:  200
[Tue Aug 16 04:11:19 CDT 2016] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120