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  • samtools picard SamFormatConverter

    Hi,

    I'm trying to run SamFormatConverter to convert a BAM to a SAM, and I'm getting an error (see below).

    The text suggests that samtools is trying to parse my BAM as a SAM. However, the file is definitely a BAM, has a '.bam' extension, and appears to have the necessary "magic number" at the top.

    Any ideas if I might be doing something wrong?

    Thanks!

    Command:
    java -jar <location>/SamFormatConverter.jar I=in.bam O=out.sam

    Head in.bam:
    BAM?@HD VN:1.0 GO:none SO:unsorted
    @SQ SN:chrM LN:16571 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:d2ed829b8a1628d16cbeee88e88e39eb SP:Homo sapiens

    Exception:
    Exception in thread "main" net.sf.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields; Line 1
    Line: BAM?@HD VN:1.0 GO:none SO:unsorted
    at net.sf.samtools.SAMTextReader.reportFatalErrorParsingLine(SAMTextReader.java:169)
    at net.sf.samtools.SAMTextReader.access$400(SAMTextReader.java:40)
    at net.sf.samtools.SAMTextReader$RecordIterator.parseLine(SAMTextReader.java:261)
    at net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:224)
    at net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:196)
    at net.sf.picard.sam.SamFormatConverter.doWork(SamFormatConverter.java:64)
    at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:150)
    at net.sf.picard.sam.SamFormatConverter.main(SamFormatConverter.java:72)

  • #2
    Hi,
    Did you figure a solution for this problem? I'm getting exactly the same error message.
    thanks.

    Comment


    • #3
      Validation_stringency=lenient

      Try VALIDATION_STRINGENCY=LENIENT in the java invocation.

      Example:

      java-Xmx67T -jar wherever/SamTowhatevernameis.jar \
      VALIDATION_STRINGENCY=LENIENT \ INPUT=uncle.sam O=nephew.sam


      That might shut up the error message and get Picard to accept the input.

      Comment


      • #4
        In this case the issue is probably the
        "BAM?" on the 1st line in front of "@HD VN:1.0 GO:none SO:unsorted"
        I would try deleting it.

        Comment

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