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  • bfast localalign error

    Hi guys,
    i am using bfast 0.7a to align SOLID PE data and got that error at bfast localalign:

    -- command used: bfast localalign -f hg19.fa -m reads.bmf -A 1 -n 8 > reads.baf

    **** Input arguments look good! *****
    ************************************************************
    ************************************************************
    Printing Program Parameters:
    programMode: [ExecuteProgram]
    fastaFileName: ~/Work_drive/Genomes/human/UCSC/BFAST_INDEX_CS/hg19.fa
    matchFileName: HGC_27.fastq.bmf
    scoringMatrixFileName: [Not Using]
    ungapped: [Not Using]
    unconstrained: [Not Using]
    space: [Color Space]
    startReadNum: 1
    endReadNum: 2147483647
    offsetLength: 20
    maxNumMatches: 384
    avgMismatchQuality: 10
    numThreads: 8
    queueLength: 25000
    timing: [Not Using]
    ************************************************************
    ************************************************************
    Reading in reference genome from /home/domine/Work_drive/Genomes/human/UCSC/BFAST_INDEX_CS/hg19.fa.nt.brg.
    In total read 25 contigs for a total of 3095693983 bases
    ************************************************************
    ************************************************************
    Reading match file from HGC_27.fastq.bmf.
    ************************************************************
    Performing alignment...
    Reads processed: 0************************************************************
    In function "AlignColorSpaceGappedConstrained": Fatal Error[OutOfRange]. Message: read and reference did not match.
    ***** Exiting due to errors *****
    -----------------------------------------------------------------------

    I have four fastq files and all of them throw an error.

    I checked the threads around and saw that it might be due to building the NT and CS brg files with different versions of BFAST but i used 0.7a for both. And the same version for building the CS indexes.

    I converted the solid reads to fastq with the solid2fastq file provided by bfast 0.7a as well. like this:

    solid2fastq readF3.csfasta readsF5-P2.csfasta readF3.qual readsF5-P2.qual.

    Have no idea what the problem could be now. Please help!!
    Thank you

  • #2
    I am sorry you are experience a problem. Could you try removing reads from your fastq until you have a small test case?

    Comment


    • #3
      Hi Nils,
      im sorry to bother you with so many problems lately.

      Update on my current problem with bfast align: I started it with -U option and like this the aligning start without complain like in my previous post. I only do not know what is the consequence of that action later. I mean how will affect the end result. Could you please explain why i could get such an error and what is the outcome of using -U?

      Thank you for your time and help

      Comment


      • #4
        It will just run slower, but you should get the same results. The error may result of malformed input in the fasta or fastq, hence why I was saying to try to reduce the fastq (or use the -s/-e in localalign) to isolate the problem. That would be helpful, as my guessing is not.

        Comment

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