Standard error
[Tue Aug 16 04:11:45 CDT 2016] picard.sam.FixMateInformation INPUT=[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/FixMateInformation/missingMate.sam] OUTPUT=/tmp/outMissingMateTest6430389012672715669sam IGNORE_MISSING_MATES=false ASSUME_SORTED=false ADD_MATE_CIGAR=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:45 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 04:11:45 FixMateInformation Sorting input into queryname order.
INFO 2016-08-16 04:11:45 FixMateInformation Sorting by queryname complete.
INFO 2016-08-16 04:11:45 FixMateInformation Output will be sorted by coordinate
INFO 2016-08-16 04:11:45 FixMateInformation Traversing query name sorted records and fixing up mate pair information.
[Tue Aug 16 04:11:45 CDT 2016] picard.sam.FixMateInformation done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1826619392
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Tue Aug 16 04:11:45 CDT 2016] picard.sam.FixMateInformation INPUT=[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/FixMateInformation/missingMate.sam] OUTPUT=/tmp/outMissingMateTest6760039196476971098sam IGNORE_MISSING_MATES=true ASSUME_SORTED=false ADD_MATE_CIGAR=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:45 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 04:11:45 FixMateInformation Sorting input into queryname order.
INFO 2016-08-16 04:11:45 FixMateInformation Sorting by queryname complete.
INFO 2016-08-16 04:11:45 FixMateInformation Output will be sorted by coordinate
INFO 2016-08-16 04:11:45 FixMateInformation Traversing query name sorted records and fixing up mate pair information.
INFO 2016-08-16 04:11:45 FixMateInformation Finished processing reads; re-sorting output file.
[Tue Aug 16 04:11:45 CDT 2016] picard.sam.FixMateInformation done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1826619392