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samtools faidx Segmentation fault

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  • #16
    Ah - blank lines at the end of the file can be easily overlooked.

    In principle I believe that faidx can cope with blank lines *between* records, but I haven't made time to work out the required code changes to do this. It would probably save some general aggravation though

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    • #17
      I had the same sort of segmentation fault. There were no blank lines in my file though. It was apparently due to one of my sequences being >65535 bp (though I don't know why that should matter).

      Maubp's biopython code took care of it nicely. Thanks!

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      • #18
        Originally posted by maubp View Post
        Just for anyone interested here is the Biopython equivalent:

        Code:
        from Bio import SeqIO
        SeqIO.convert("inputfilename.fas", "fasta", "outputfilename.fas", "fasta")
        The convert function returns the number of records if you wanted that information.
        Thank you for this. Just ran into this problem.

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        • #19
          Originally posted by baohua100 View Post
          $ ./samtools faidx /media/Poplar/baohua/genome/poplar_genome.fa
          [fai_build_core] different line length in sequence 'scaffold_28'.
          The problem with scaffold_28 in this file was the same problem that was reported here. It has now been fixed, and the fix will appear in samtools (and htslib) 1.3.

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          • #20
            Easiest way to fix this is to use seqret in emboss. Just convert the fasta file to ncbi style fasta and it automatically fixes the issue.

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