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  • Assertion failed error in BFAST localalign

    Hi all, I'm getting the following error when trying to combine bfast and bwa mapped reads. Any suggestions would be appreciated.

    command:
    bfast localalign -f rna.fasta -1 p1.f3.reads.bmf -2 p1.f5.reads.bfm -A 1 -t -U -n 4 > p1.reads.baf

    error:
    Assertion failed: (0 == strcmp(m->readName, r2_name)), function RGMatchesRead_2bmf, file RGMatches.c, line 51.
    Abort trap
    Assertion failed: (0 == strcmp(m->readName, r2_name)), function RGMatchesRead_2bmf, file RGMatches

  • #2
    Looks like your reads are not in the same order within the two files (also p1.f5.reads.bfm should be p1.f5.read.bmf). Take a look at your input FASTQ files to make sure the read names are in the same order.

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    • #3
      The first and last 100 lines of reads are in the same order. I've renamed the f5 files to bmf (which was a typo when making the files). Could that be responsible?

      Comment


      • #4
        Changed the name and still the same error. How could I ensure that all the names are in the same order?

        Comment


        • #5
          Where are you getting your FASTQ from?

          Comment


          • #6
            From the solid2fastq script that came with bfast+bwa. I made a seperate fastq for each of the F3 and F5 reads rather than paired.

            Comment


            • #7
              Ah, you have to make them together. You cannot convert them unpaired then input them as paired.

              Comment


              • #8
                Oh, I was following the flow from here: http://seqanswers.com/forums/showthr...ight=bfast+bwa

                So, you make the fastq paired, then map using the same fastq file for the f3 and f5 seperately?

                Comment

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