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  • mpileup on 300 BAM files

    I have seen similar posts on this forum, but I continue getting "segmentation fault" every time I start mpileup on my BAM files. I have about 300 BAM files from Exome sequencing of high depth.

    samtools-0.1.18/samtools mpileup -BEDf ref/hg19.fa -d 200 -q 20 -r chr2 -b bamFiles > mpileups/kirc.exome.q20.chr2.m.pileup

    [bam_header_read] EOF marker is absent. The input is probably truncated.

    [bam_header_read] EOF marker is absent. The input is probably truncated.
    Segmentation fault

    What is the solution ?
    Thanks.
    Last edited by tejajo; 07-08-2013, 02:33 AM.

  • #2
    Segmentation faults are often due to insufficient memory in the computer. The sorting process requests too much memory based on the size of the files involved. Try a more powerful computer.

    Comment


    • #3
      Have you checked if this warning from samtools is actually true? It can happen if a BAM file is only partially copied for example.

      Code:
      [bam_header_read] EOF marker is absent. The input is probably truncated.
      Corrupt data could easily be causing the segmentation fault.

      Note there is a bug in samtools 0.1.19 where this warning can appear by mistake when using Unix pipes - https://github.com/samtools/samtools/issues/18

      Comment

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