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  • About Segfault in samtools

    Hi all,
    I encounted a question about segmentation fault when I used the tool of samtools(command:faidx). I checked the resourse with the command of "dmesg", the result is shown in the picture below.
    who had encounted this problem,please help me. Thanks
    Attached Files

  • #2
    Can you provide additional info? What OS is this on? Did you compile samtools yourself? How much memory do you have?

    Comment


    • #3
      Originally posted by GenoMax View Post
      Can you provide additional info? What OS is this on? Did you compile samtools yourself? How much memory do you have?
      Hi GenoMax,
      Thanks for your reply. My OS is Linux Radhat. I would like to use the faidx command of samtools when encounted this question. But the others command of samtools is good. The memory of server is 127G. So, I don't know why. The below pictures are the command I moved and the memory of the server.
      Attached Files

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      • #4
        One simple thing to check... Do you have line breaks in your fasta? And are you sure they are all at regular intervals?

        I think I might have had problems with faidx when I had one giant contig of DNA with no line breaks, or if I made a multi-entry fasta, and the lines had differeet lengths.

        Comment


        • #5
          Originally posted by swbarnes2 View Post
          One simple thing to check... Do you have line breaks in your fasta? And are you sure they are all at regular intervals?

          I think I might have had problems with faidx when I had one giant contig of DNA with no line breaks, or if I made a multi-entry fasta, and the lines had differeet lengths.
          Thanks for your reply. I check my fasta file according your advice, but it became empty file and I don't know why. So I input the fasta again, then it had done. Thanks again.

          Comment


          • #6
            Originally posted by GenoMax View Post
            Can you provide additional info? What OS is this on? Did you compile samtools yourself? How much memory do you have?
            Now I had solved my question. The problem is my fasta file. It became a empty file in my server. I don't know why. However thanks a lot.

            Comment

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