Standard error
[Tue Aug 16 04:11:25 CDT 2016] picard.analysis.CollectRrbsMetrics INPUT=testdata/picard/metrics/chrMReads.sam METRICS_FILE_PREFIX=/tmp/crmt.6331107865603941240.tmp/READ_TEST REFERENCE=testdata/picard/metrics/chrM.reference.fasta MINIMUM_READ_LENGTH=5 C_QUALITY_THRESHOLD=20 NEXT_BASE_QUALITY_THRESHOLD=10 MAX_MISMATCH_RATE=0.1 ASSUME_SORTED=false METRIC_ACCUMULATION_LEVEL=[ALL_READS] 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/script1703560014383571046.R /tmp/crmt.6331107865603941240.tmp/READ_TEST.rrbs_detail_metrics /tmp/crmt.6331107865603941240.tmp/READ_TEST.rrbs_summary_metrics /tmp/crmt.6331107865603941240.tmp/READ_TEST.rrbs_qc.pdf
INFO 2016-08-16 04:11:26 ProcessExecutor null device
INFO 2016-08-16 04:11:26 ProcessExecutor 1
[Tue Aug 16 04:11:26 CDT 2016] picard.analysis.CollectRrbsMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1829765120