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  • BFAST memory error in postprocess

    Hello, I have a set of 85-bp long solexa reads and I have already used BFAST match, local align, an postprocess (with -a 3 option) successfully.

    I am now trying to filter the multi reads using the -a 4 option and am getting a memory error message.

    This is the command I am using:

    /bfast postprocess -f /filepath/TAIR9_chr_all.fas -i /filepath/bfast.aligned.split1_1_ZT0.baf -a 4 -O 1 > /filepath/bfast.reported.split1_1_ZT0.sam

    This is the error message I am getting:

    **********************************************************
    Checking input parameters supplied by the user ...
    Validating fastaFileName /filepath/TAIR9_chr_all.fas.
    Validating alignFileName /filepath/bfast.aligned.split1.baf.
    Input arguments look good!
    **********************************************************
    **********************************************************
    Printing Program Parameters:
    programMode: [ExecuteProgram]
    fastaFileName: /filepath/TAIR9_chr_all.fas
    alignFileName: /filepath/bfast.aligned.split1.baf
    algorithm: [Best Score All]
    space: [NT Space]
    unpaired: [Not Using]
    reversePaired: [Not Using]
    avgMismatchQuality: 10
    scoringMatrixFileName: [Not Using]
    randomBest: [Not Using]
    minMappingQuality: -2147483648
    minNormalizedScore: -2147483648
    pairingStandardDeviation: 2.000000
    gappedPairingRescue [Not Using]
    numThreads: 1
    queueLength: 50000
    outputFormat: [SAM]
    outputID: [Not Using]
    RGFileName: [Not Using]
    timing: [Not Using]
    ************************************************************
    ************************************************************
    Reading in reference genome from /filepath/TAIR9_chr_all.fas.nt.brg.
    In total read 7 contigs for a total of 119667750 bases
    ************************************************************
    Postprocessing...
    ************************************************************
    In function "AlignedEntryRead": Fatal Error[MallocMemory]. Variable/Value: a->alnRead.
    Message: Could not allocate memory.
    ***** Exiting due to errors *****

    This is the message I am getting with just this specific file. With other split file I am getting the message "line 3: 1182 Segmentation fault" (although the line is different depending on the file)

    I cannot figure out what this means and would appreciate any advice!

    Thanks,
    Marisa
    Last edited by Marisa_Miller; 09-17-2010, 10:58 AM.

  • #2
    Try posting a test case to the bfast help mailing list ([email protected]). I would be happy to help over there.

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    • #3
      I am not sure if this could be the problem, but it may be that I did all the other processing with version d and I am now using version e for the step in my above post? I will try doing everything with the new version for just one of my 12 libraries to see if it works.

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      • #4
        It could be. Use definitely the latest version. If you still have the problem send over some data so the bug can be track down.
        -drd

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