htsjdk.samtools.SAMFormatException: Error parsing SAM header. Problem parsing @PG key:value pair ID:redacted clashes with ID:bwa. Line: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:/export/local/tools/bwa/bwa mem -t 32 -R @RG ID:redacted SM:redacted LB:1 PL:Illumina PM:Miseq PU:MiseqSN.1 CN:OSU /export/local/ref/indices/bwa/grch37/grch37 cutadapt/redacted_R1.fastq cutadapt/redacted_R2.fastq; File /home/x/capture/aligned_grch37/redacted.bam; Line number 88

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via GitHub by jblachly
, 1 year ago
Error parsing SAM header. Problem parsing @PG key:value pair ID:redacted clashes with ID:bwa. Line: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:/export/local/tools/bwa/bwa mem -t 32 -R @RG ID:redacted SM:redacted LB:1 PL:Illumina
via GitHub by johnbradley
, 3 months ago
Error parsing SAM header. Problem parsing @PG key:value pair ID:1 clashes with ID:bwa. Line: @PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa mem -R @RG ID:1 LB:LIBRARY PL:illumina SM:sample1 PU:AB1234 -t 8 /var/lib/cwl/stge2216d72-3f93-4c68
via GitHub by danarte
, 9 months ago
Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1; ; Line number 3
htsjdk.samtools.SAMFormatException: Error parsing SAM header. Problem parsing @PG key:value pair ID:redacted clashes with ID:bwa. Line: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:/export/local/tools/bwa/bwa mem -t 32 -R @RG ID:redacted SM:redacted LB:1 PL:Illumina PM:Miseq PU:MiseqSN.1 CN:OSU /export/local/ref/indices/bwa/grch37/grch37 cutadapt/redacted_R1.fastq cutadapt/redacted_R2.fastq; File /home/x/capture/aligned_grch37/redacted.bam; Line number 88
at htsjdk.samtools.SAMTextHeaderCodec.reportErrorParsingLine(SAMTextHeaderCodec.java:238)
at htsjdk.samtools.SAMTextHeaderCodec.access$200(SAMTextHeaderCodec.java:43)
at htsjdk.samtools.SAMTextHeaderCodec$ParsedHeaderLine.(SAMTextHeaderCodec.java:293)
at htsjdk.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:87)
at htsjdk.samtools.BAMFileReader.readHeader(BAMFileReader.java:524)
at htsjdk.samtools.BAMFileReader.(BAMFileReader.java:177)
at htsjdk.samtools.BAMFileReader.(BAMFileReader.java:132)
at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:293)
at picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:110)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

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