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  • Samtools faidx errors

    Hi,

    I am new to samtools and bioinformatics in general. I have a quick question about generating a fasta index file from a .fa file. I see a segmentation fault while running samtools faidx on hg19:

    $samtools faidx hg19.fa
    [fai_build_core] different line length in sequence 'chr1'.
    Segmentation fault

    This is probably a dumb question, but what could be causing this?

    Thanks!

  • #2
    You have differing line lengths after chromosome one. Check that each line in chr1 has the same length (except for the last, which should be equal to or shorter).

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    • #3
      Thanks - I didn't know that every line had to be the same length.

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      • #4
        samtools faidx hg19.fa
        [fai_build_core] different line length in sequence 'chrY'

        hi i have the same problem.....can you tell how can i correct the length?? i am very new to these stuff

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