bamstat step did not produce desired output even reported "completed Success"

[QuanliWang]

[job bamstat] /home/ec2-user/cwltool/h3agatk/test/working/workinglNOWqB$ docker \ run \ -i \ --volume=/home/ec2-user/cwltool/h3agatk/test/working/working54BLcY/samtools-sort-2017-04-23.bam:/var/lib/cwl/stgdabe04bb-94a4-4a62-8ccf-485566c3b108/samtools-sort-2017-04-23.bam:ro \ --volume=/home/ec2-user/cwltool/h3agatk/test/working/workinglNOWqB:/var/spool/cwl:rw \ --volume=/home/ec2-user/cwltool/h3agatk/test/working/workingLwio_7:/tmp:rw \ --workdir=/var/spool/cwl \ --read-only=true \ --user=500 \ --rm \ --env=TMPDIR=/tmp \ --env=HOME=/var/spool/cwl \ quay.io/briandoconnor/dockstore-tool-bamstats:1.25-7 \ bash \ /usr/local/bin/bamstats \ 4 \ /var/lib/cwl/stgdabe04bb-94a4-4a62-8ccf-485566c3b108/samtools-sort-2017-04-23.bam ERROR: unexpected error encountered - Error parsing SAM header. Problem parsing @PG key:value pair ID:NA12878_test_sample clashes with ID:bwa. Line: @PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa mem -R @RG ID:NA12878_test_sample PL:ILLUMINA PU:pu LB:group1 SM:SAMPLEID -t 16 /var/lib/cwl/stg3e9984bd-fb25-452e-92c8-1d625087ff38/genome.fa /var/lib/cwl/stg1dbe13bc-df10-449d-a043-4693682b4e52/NA12878.R1.fastq.gz /var/lib/cwl/stg4f51649d-f2b8-4b18-a415-98665b161281/NA12878.R2.fastq.gz; File /var/lib/cwl/stgdabe04bb-94a4-4a62-8ccf-485566c3b108/samtools-sort-2017-04-23.bam; Line number 96 net.sf.samtools.SAMFormatException: Error parsing SAM header. Problem parsing @PG key:value pair ID:NA12878_test_sample clashes with ID:bwa. Line: @PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa mem -R @RG ID:NA12878_test_sample PL:ILLUMINA PU:pu LB:group1 SM:SAMPLEID -t 16 /var/lib/cwl/stg3e9984bd-fb25-452e-92c8-1d625087ff38/genome.fa /var/lib/cwl/stg1dbe13bc-df10-449d-a043-4693682b4e52/NA12878.R1.fastq.gz /var/lib/cwl/stg4f51649d-f2b8-4b18-a415-98665b161281/NA12878.R2.fastq.gz; File /var/lib/cwl/stgdabe04bb-94a4-4a62-8ccf-485566c3b108/samtools-sort-2017-04-23.bam; Line number 96 at net.sf.samtools.SAMTextHeaderCodec.reportErrorParsingLine(SAMTextHeaderCodec.java:230) at net.sf.samtools.SAMTextHeaderCodec.access$100(SAMTextHeaderCodec.java:39) at net.sf.samtools.SAMTextHeaderCodec$ParsedHeaderLine.(SAMTextHeaderCodec.java:280) at net.sf.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:80) at net.sf.samtools.BAMFileReader.readHeader(BAMFileReader.java:364) at net.sf.samtools.BAMFileReader.(BAMFileReader.java:118) at net.sf.samtools.BAMFileReader.(BAMFileReader.java:97) at net.sf.samtools.SAMFileReader.init(SAMFileReader.java:504) at net.sf.samtools.SAMFileReader.(SAMFileReader.java:165) at net.sf.samtools.SAMFileReader.(SAMFileReader.java:120) at nestor.tools.BAMStats.(BAMStats.java:390) at nestor.tools.BAMStats.main(BAMStats.java:259) adding: bamstats_report.html (stored 0%) adding: bamstats_report.html.data/ (stored 0%) [job bamstat] completed success [job bamstat] { "bamstats_report": { "format": "http://edamontology.org/format_3615", "checksum": "sha1$9534d00fc3c12d79f2c284b78eeb89474df61f23", "basename": "bamstats_report.zip", "location": "file:///home/ec2-user/cwltool/h3agatk/test/working/workinglNOWqB/bamstats_report.zip", "class": "File", "size": 370 } }