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  • #16
    Thanks Sacrolfur, I'll give that a try.

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    • #17
      Try to use both commands separately and write output here.

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      • #18
        using -u when running samtools mpileup

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        • #19
          I got the same problem. I tried the verson 1.0, 0.1.19, 0.1.18 and none worked.
          Any one can help to solve this problem.

          Here are my command and error message:

          samtools mpileup -ugf F.fna F.sorted.bam > F.bcf
          [mpileup] 1 samples in 1 input files
          <mpileup> Set max per-file depth to 8000
          [bcf_sync] incorrect number of fields (6 != 5) at 67:234
          Segmentation fault

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          • #20
            I figure out it problem by update the bcftools from 0.1.17 to 1.1.

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            • #21
              hello,all,I think I have solve this problem:
              both nohup and ">" would add stdout and stderr to output file,which cause that problem。

              so,
              "samtools mpileup -ugf F.fna F.sorted.bam -o F.bcf"
              instead of
              "samtools mpileup -ugf F.fna F.sorted.bam > F.bcf"

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              • #22
                Same here, the bcftools that is compiled within samtools is old, and when I compiled a fresh version from github, this error vanished.
                Sam Hokin
                Computational Scientist, Carnegie and NCGR

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