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[Picard] Read error; BinaryCodec in readmode
Dear, GATK team.
Could I ask something related to picard program in here?
java -Dsamjdk.compression_level=5 -Xms16000m -jar /BiO/BioTools/picard-2.17.8/picard.jar \ SortSam \ INPUT=/BiO/Project/brandon-genome-analysis/wdl/cromwell-executions/PreProcessingForVariantDiscovery_GATK4/9dccfb10-f6c1-4d03-b74f-14f2d3dce600/call-SortAndFixTags/inputs/BiO/Project/brandon-genome-analysis/wdl/cromwell-executions/PreProcessingForVariantDiscovery_GATK4/9dccfb10-f6c1-4d03-b74f-14f2d3dce600/call-MarkDuplicates/execution/NA12878.hg38.aligned.unsorted.duplicates_marked.bam \ OUTPUT=/dev/stdout \ SORT_ORDER="coordinate" \ CREATE_INDEX=false \ CREATE_MD5_FILE=false \ | \ java -Dsamjdk.compression_level=5 -Xms2000m -jar /BiO/BioTools/picard-2.17.8/picard.jar \ SetNmAndUqTags \ INPUT=/dev/stdin \ OUTPUT=NA12878.hg38.aligned.duplicate_marked.sorted.bam \ CREATE_INDEX=true \ CREATE_MD5_FILE=true \ REFERENCE_SEQUENCE=/BiO/Project/brandon-genome-analysis/wdl/cromwell-executions/PreProcessingForVariantDiscovery_GATK4/9dccfb10-f6c1-4d03-b74f-14f2d3dce600/call-SortAndFixTags/inputs/BiO/Project/brandon-genome-analysis/ref/ftp.broadinstitute.org/bundle/hg38/Homo_sapiens_assembly38.fasta
This piping command is not work in my case.
When I divided the command and run, it was work well.
so, I guess this problem is related to picard.
How can I handle this problem?