htsjdk.samtools.SAMFormatException

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  • GitHub comment 614#222395370
    via GitHub by jrobinso
    ,
    • 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.<init>(SAMTextHeaderCodec.java:293) at htsjdk.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:87) at htsjdk.samtools.BAMFileReader.readHeader(BAMFileReader.java:524) at htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:177) at htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:132) at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:293) at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:145) 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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