Hello,

I've been running github.com/gatk-workflows/gatk4-data-processing/processing-for-variant-discovery-gatk4:2.1.0 and the MergeBamAlignment task fails with the following stderr output:

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.03a1590e
19:22:08.740 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.2.4.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Thu Mar 31 19:22:08 GMT 2022] MergeBamAlignment --UNMAPPED_BAM /cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/6659022c-0aae-4e65-a176-5e3174479364/sort_sam/3e713703-04e5-4862-97b9-f0e008d7c57e/call-sort_sam/cacheCopy/POL_FAM10_1.unmapped.bam --ALIGNED_BAM /cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/4d1a6cef-461a-4421-9f08-d957de504ae0/PreProcessingForVariantDiscovery_GATK4/6711ea4e-0e54-4ab5-bbd3-cf5cea8d3073/call-SamToFastqAndBwaMem/shard-0/POL_FAM10_1.unmapped.unmerged.bam --OUTPUT POL_FAM10_1.unmapped.aligned.unsorted.bam --PROGRAM_RECORD_ID bwamem --PROGRAM_GROUP_VERSION 0.7.15-r1140 --PROGRAM_GROUP_COMMAND_LINE bwa mem -K 100000000 -p -v 3 -t 16 -Y /cromwell_root/gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta --PROGRAM_GROUP_NAME bwamem --PAIRED_RUN true --CLIP_ADAPTERS false --IS_BISULFITE_SEQUENCE false --ALIGNED_READS_ONLY false --MAX_INSERTIONS_OR_DELETIONS -1 --ATTRIBUTES_TO_RETAIN X0 --EXPECTED_ORIENTATIONS FR --ALIGNER_PROPER_PAIR_FLAGS true --SORT_ORDER unsorted --PRIMARY_ALIGNMENT_STRATEGY MostDistant --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS true --UNMAPPED_READ_STRATEGY COPY_TO_TAG --VALIDATION_STRINGENCY SILENT --MAX_RECORDS_IN_RAM 2000000 --REFERENCE_SEQUENCE /cromwell_root/gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta --ADD_PG_TAG_TO_READS true --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --READ1_TRIM 0 --READ2_TRIM 0 --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Mar 31 19:22:09 GMT 2022] Executing as root@6741cafb4776 on Linux 5.10.90+ amd64; OpenJDK 64-Bit Server VM 1.8.0_242-8u242-b08-0ubuntu3~18.04-b08; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.2.4.0
INFO	2022-03-31 19:22:10	SamAlignmentMerger	Processing SAM file(s): [/cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/4d1a6cef-461a-4421-9f08-d957de504ae0/PreProcessingForVariantDiscovery_GATK4/6711ea4e-0e54-4ab5-bbd3-cf5cea8d3073/call-SamToFastqAndBwaMem/shard-0/POL_FAM10_1.unmapped.unmerged.bam]
[Thu Mar 31 19:22:10 GMT 2022] picard.sam.MergeBamAlignment done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=3113877504
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
picard.PicardException: Program Record ID already in use in unmapped BAM file.
	at picard.sam.AbstractAlignmentMerger.mergeAlignment(AbstractAlignmentMerger.java:394)
	at picard.sam.SamAlignmentMerger.mergeAlignment(SamAlignmentMerger.java:181)
	at picard.sam.MergeBamAlignment.doWork(MergeBamAlignment.java:368)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
	at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37)
	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
	at org.broadinstitute.hellbender.Main.main(Main.java:289)
Using GATK jar /gatk/gatk-package-4.2.4.0-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Dsamjdk.compression_level=5 -Xms3G -jar /gatk/gatk-package-4.2.4.0-local.jar MergeBamAlignment --VALIDATION_STRINGENCY SILENT --EXPECTED_ORIENTATIONS FR --ATTRIBUTES_TO_RETAIN X0 --ALIGNED_BAM /cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/4d1a6cef-461a-4421-9f08-d957de504ae0/PreProcessingForVariantDiscovery_GATK4/6711ea4e-0e54-4ab5-bbd3-cf5cea8d3073/call-SamToFastqAndBwaMem/shard-0/POL_FAM10_1.unmapped.unmerged.bam --UNMAPPED_BAM /cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/6659022c-0aae-4e65-a176-5e3174479364/sort_sam/3e713703-04e5-4862-97b9-f0e008d7c57e/call-sort_sam/cacheCopy/POL_FAM10_1.unmapped.bam --OUTPUT POL_FAM10_1.unmapped.aligned.unsorted.bam --REFERENCE_SEQUENCE /cromwell_root/gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta --PAIRED_RUN true --SORT_ORDER unsorted --IS_BISULFITE_SEQUENCE false --ALIGNED_READS_ONLY false --CLIP_ADAPTERS false --MAX_RECORDS_IN_RAM 2000000 --ADD_MATE_CIGAR true --MAX_INSERTIONS_OR_DELETIONS -1 --PRIMARY_ALIGNMENT_STRATEGY MostDistant --PROGRAM_RECORD_ID bwamem --PROGRAM_GROUP_VERSION 0.7.15-r1140 --PROGRAM_GROUP_COMMAND_LINE bwa mem -K 100000000 -p -v 3 -t 16 -Y /cromwell_root/gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta --PROGRAM_GROUP_NAME bwamem --UNMAPPED_READ_STRATEGY COPY_TO_TAG --ALIGNER_PROPER_PAIR_FLAGS true --UNMAP_CONTAMINANT_READS true

Any ideas? Thanks!

Best, Oliver