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  • Bfast localalign error

    I am Pooja working as an intern in Ganit labs in Bangalore, on NGS .

    I was trying to run bfast for paired end alignment using bfast (bfast+bwa-0.6.4e) and I am getting the following error in the localalign step

    The error looks like this:

    bfast: AlignNTSpace.c:165: AlignNTSpaceGappedConstrained: Assertion `0 <= endRowStepOne && 0 <= endColStepOne' failed.

    command used for localalign was:

    /Apps/serial/bfast+bwa/bin/bfast localalign -f hg_18.fa -n 8 -M 1280 -A 0 -O bfast.bwaaln_20-T_3_3_1_sequence.fastq.bmf -T bfast.bwaaln_20T_3_3_2_sequence.bmf > bfast.la_20-T_3_3_sequence_te.baf

    I have all the files like .brg file and all the indexed(.bif) files present in the working directory.
    Also I have used bwaaln to generate the match (.bmf) files.

    Thank you

  • #2
    Can you add -U and try again?
    -drd

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