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  • bwa aln fails

    I'm running bwa verision 0.5.9

    I have 6 fastq files each 33 GB.

    I'm running:

    bwa aln -l 28 -t 6 <ref_file> <in_file> -f <out_file>

    Four of the six fastq files align to the indexed genome correctly. All six files were generated from the same library, adapters have been clipped. However 2 fastq files run through:

    [bwa_aln] 17bp reads: max_diff = 2
    [bwa_aln] 38bp reads: max_diff = 3
    [bwa_aln] 64bp reads: max_diff = 4
    [bwa_aln] 93bp reads: max_diff = 5
    [bwa_aln] 124bp reads: max_diff = 6
    [bwa_aln] 157bp reads: max_diff = 7
    [bwa_aln] 190bp reads: max_diff = 8
    [bwa_aln] 225bp reads: max_diff = 9

    then stall here (for hours) like its frozen. I'm not getting a segmentation fault or any error. The program just ceases to continue.

    Has anybody seen this before or have a fix???

  • #2
    First reasonable check, are those two really look the same as the other four? If it's fastq.gz, unzip it first, then head or tail on it.

    Comment


    • #3
      Are you running them at the same time, if so try to rerun the 2 files separately?
      Thanks,

      Comment


      • #4
        How big is your machine?
        Have you checked your inputs?
        Bad input and/or not enough memory causes problems with BWA.

        See my response in this thread for an explanation:
        Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

        Comment


        • #5
          Well, not really sure what I did. I changed my pbs script, dropped number of threads from 6 to 4 and it seems to be running....whatever works man.

          Comment

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