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

GitHub | jblachly | 4 months ago
  1. 0

    @PG ID:bwa line containing @RG ID:... causes SAMFormatException

    GitHub | 4 months ago | jblachly
    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
  2. 0

    SamReaderFactory fails to return CRAMReader for http resource

    GitHub | 6 months ago | jrobinso
    htsjdk.samtools.SAMFormatException: Unrecognized file format: org.broad.igv.util.stream.IGVSeekableBufferedStream@77b52d12
  3. 0

    GitHub comment 614#222395370

    GitHub | 6 months ago | jrobinso
    htsjdk.samtools.SAMFormatException: Unrecognized file format: org.broad.igv.util.stream.IGVSeekableBufferedStream@1613674b
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  5. 0

    GitHub comment 2#174816922

    GitHub | 10 months ago | brentp
    htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Tag of type i should have signed decimal value; File /dev/stdin; Line 247729 Line: HISEQ:318:H25NKADXY:1:2210:5526:37163 675 chr1 11167510 60 107M13S = 11167604 220 AAAAAACGTGATGGGCACATCTGGGCCTCCAGTTACCAGAAAGGGCACCTAAGAAGGCAGAAGGAAAAGGAATATTTTAATATTTTGAGCTCCTTCAAAGGTTTACAAGGAAACCTGGAA<)?77<AA5?A***5A>1?===<0=ABA############################################################################################ NM:i:3 MD:Z:62A19A8T15 AS:i:92 XS:i:20 RG:Z:769P_AH25NKADXY_L001 BC:Z:AGGGGG OP:i:11167510 XI:i:None XO:Z:AAAAAACGTGATGGGCACATCTGGGCCTCCAGTTACCAGAAAGGGCACCTAAGAAGGCAGAAGGAAAAGGAATATTTTAATATTTTGAGCTCCTTCAAAGGTTTACAAGGAAACCTGGAA OC:Z:107M13S
  6. 0

    VcfBreakendToReadPair writes SAMRecords extending outside of chromosome boundries

    GitHub | 2 months ago | ayhand
    htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Read name gridss57046, Read CIGAR M operator maps off end of reference

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    Root Cause Analysis

    1. 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()
    2. HTS JDK
      SamReaderFactory$SamReaderFactoryImpl.open
      1. htsjdk.samtools.SAMTextHeaderCodec.reportErrorParsingLine(SAMTextHeaderCodec.java:238)
      2. htsjdk.samtools.SAMTextHeaderCodec.access$200(SAMTextHeaderCodec.java:43)
      3. htsjdk.samtools.SAMTextHeaderCodec$ParsedHeaderLine.<init>(SAMTextHeaderCodec.java:293)
      4. htsjdk.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:87)
      5. htsjdk.samtools.BAMFileReader.readHeader(BAMFileReader.java:524)
      6. htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:177)
      7. htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:132)
      8. htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:293)
      9. htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:145)
      9 frames
    3. picard.analysis.directed
      CollectTargetedMetrics.doWork
      1. picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:110)
      1 frame
    4. picard.cmdline
      PicardCommandLine.main
      1. picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
      2. picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
      3. picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
      3 frames