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  • BFAST match abort trap

    Hello,

    I am trying to analyze SOLiD data using BFAST, and am a little new to the system. I have successfully created and indexed the reference genome, but I am running into problems with BFAST match. I get an error message saying:

    Reading /ResearchFiles/JEC21_genome/CNA_assembly/BFAST/NIH433_fastq_reads.1.fastq into a temp file.
    Assertion failed: (m->readLength > 0), function RGMatchPrint, file ../bfast/RGMatch.c, line 155.
    Abort trap

    My command line is bfast match -f JEC21_all.fasta -r NIH433_fastq_reads.1.fastq > NIH433_JEC21_matched

    I also created the input fastq file using the solid2fastq program that came with the BFAST package.

    Any idea what is causing this?

    Thanks,

    BB

  • #2
    Most likely the input fastq is corrupted. You can either try to re-run solid2fastq, or remove reads from the input fastq until you find the offending read.

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