Standard error
[Thu Apr 24 13:04:07 EDT 2025] FixMateInformation --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/FixMateInformation/missingMate.sam --OUTPUT /tmp/outMissingMateTest285609804329573720sam --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 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:04:07 FixMateInformation Sorting input into queryname order.
INFO 2025-04-24 13:04:07 FixMateInformation Sorting by queryname complete.
INFO 2025-04-24 13:04:07 FixMateInformation Output will be sorted by coordinate
INFO 2025-04-24 13:04:07 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/outMissingMateTest285609804329573720sam
INFO 2025-04-24 13:04:07 FixMateInformation Traversing query name sorted records and fixing up mate pair information.
[Thu Apr 24 13:04:07 EDT 2025] picard.sam.FixMateInformation done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:07 EDT 2025] FixMateInformation --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/FixMateInformation/missingMate.sam --OUTPUT /tmp/outMissingMateTest6264506292132347173sam --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 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:04:07 FixMateInformation Sorting input into queryname order.
INFO 2025-04-24 13:04:07 FixMateInformation Sorting by queryname complete.
INFO 2025-04-24 13:04:07 FixMateInformation Output will be sorted by coordinate
INFO 2025-04-24 13:04:07 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/outMissingMateTest6264506292132347173sam
INFO 2025-04-24 13:04:07 FixMateInformation Traversing query name sorted records and fixing up mate pair information.
INFO 2025-04-24 13:04:07 FixMateInformation Finished processing reads; re-sorting output file.
[Thu Apr 24 13:04:07 EDT 2025] picard.sam.FixMateInformation done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824