Standard error
[Thu Apr 24 13:04:08 EDT 2025] MergeSamFiles --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeSamFiles/unsorted_input/1.sam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeSamFiles/unsorted_input/2.sam --OUTPUT /tmp/unsortedInputSortedOutputTest.5814606776839259317.bam --SORT_ORDER coordinate --CREATE_INDEX true --ASSUME_SORTED false --MERGE_SEQUENCE_DICTIONARIES false --USE_THREADING false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:08 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 13:04:08 MergeSamFiles Sorting input files using temp directory [/tmp/root]
INFO 2025-04-24 13:04:08 MergeSamFiles Finished reading inputs.
[Thu Apr 24 13:04:08 EDT 2025] picard.sam.MergeSamFiles done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:08 EDT 2025] ValidateSamFile --INPUT /tmp/unsortedInputSortedOutputTest.5814606776839259317.bam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --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 13:04:08 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
WARNING 2025-04-24 13:04:08 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:08 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824