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  • robertthebob1
    Junior Member
    • May 2013
    • 2
    #1

    BFAST, Could not read in buffer

    I'm having some problem getting started with Bfast:
    bob@homequad:/home2/NGS/tmp$ bfast index -n 8 -f /home2/NGS/ref/yeast/seq/S288C_reference_sequence_R64-1-1_20110203.fasta -m 111111111111111111 -w 18 -i 1
    ************************************************************
    Checking input parameters supplied by the user ...
    Validating fastaFileName /home2/NGS/ref/yeast/seq/S288C_reference_sequence_R64-1-1_20110203.fasta.
    Validating tmpDir path ./.
    Input arguments look good!
    ************************************************************
    ************************************************************
    Printing Program Parameters:
    programMode: [ExecuteProgram]
    fastaFileName: /home2/NGS/ref/yeast/seq/S288C_reference_sequence_R64-1-1_20110203.fasta
    space: [NT Space]
    mask: 111111111111111111
    depth: 0
    hashWidth: 18
    indexNumber: 1
    repeatMasker: [Not Using]
    startContig: 0
    startPos: 0
    endContig: 2147483647
    endPos: 2147483647
    exonsFileName: [Not Using]
    numThreads: 8
    tmpDir: ./
    timing: [Not Using]
    ************************************************************
    ************************************************************
    Reading in reference genome from /home2/NGS/ref/yeast/seq/S288C_reference_sequence_R64-1-1_20110203.fasta.nt.brg.
    In total read 17 contigs for a total of 12157105 bases
    ************************************************************
    Creating the index...
    ************************************************************
    Warning: startContig was less than zero.
    Defaulting to contig=1 and position=1.
    ************************************************************
    ************************************************************
    Warning: endContig was greater than the number of contigs in the reference genome.
    Defaulting to reference genome's end contig=17 and position=85779.
    ************************************************************
    Currently on [contig,pos]:
    [------17,------85779]
    Sorting by thread...
    24.998 percent complete************************************************************
    In function "RGIndexMergeHelperFromDiskGetNext_8": Fatal Error[ReadFileError]. Message: Could not read in buffer.
    The file stream error was:: Bad file descriptor
    ***** Exiting due to errors *****
    ************************************************************
    bob@homequad:/home2/NGS/tmp$

    I've looked at the source and can't see right away what the problem
    might be. May I ask for Nils' help?
    Robert Williams
    Tags: bfast
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