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  • Bfast alignment error

    The command I am using is :
    "./bfast-0.7.0/bin/bfast match -f human_g1k_v37.fa -r part2.fa > test.bmf"

    The human_g1k_v37.fa has been indexed.

    Error Message:
    “In function "RGIndexReadHeader": Fatal Error[ReadFileError]. Message: Could not read header.”

    Dose somebody have encountered this error? Or can you give some ideas on what may be the reason for this error?

    The input is indexed fasta and fastq. I don't think there is read header in these inputs. Read header, as I know, appears in SAM or BAM format files, which are output of alignment. But now I am working on alignment, how can the inputs have read header. It's strange.

  • #2
    It means "read" as in trying to "read" the header, not the noun read

    There is not enough information to diagnose the problem.

    Comment


    • #3
      Thanks for your pointing out "read" is a verb . I have to admit my poor English reading.

      "There is not enough information to diagnose the problem." Actually, all information I know related to this problem was listed. I have emailed to authors of this software, but haven't received any answer.

      So except hacking the source code, I don't have other approaches yet.

      Comment


      • #4
        I am the author of the software. Unfortunately, I maintain this software on my free time and my free time has asymptotically approached zero lately so I have been unable to debug the software. Also, I don't have a machine that can index a human genome at home, so perhaps I should start a donation drive to get one and better support BFAST users?

        Comment

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