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  • jfk
    Junior Member
    • Jul 2011
    • 5
    #1

    Bfast match .bmf? file - anybody seen .bmf? before

    Hi everyone

    I've used BFAST (0.7.0a) before on our institute computing cluster successfully before, however, after running 'bfast match' last night I have a '.bmf?' file instead of the normal '.bmf' file.

    Has anybody else observed this?

    bfast match seems to have executed correctly, my .fastq file is 2.3GB and the .bmf? file is 1.3GB.

    I am analysing SOLiD whole genome resequencing data of yeast strain.

    bfast match output below (I've #'d out some of the path details on purpose):

    ************************************************************
    Checking input parameters supplied by the user ...
    Validating fastaFileName ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.
    Validating readsFileName PYR4b.fastq.
    Validating tmpDir path ./.
    **** Input arguments look good!
    ************************************************************
    ************************************************************
    Printing Program Parameters:
    programMode: [ExecuteProgram]
    fastaFileName: ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa
    mainIndexes [Auto-recognizing]
    secondaryIndexes [Not Using]
    readsFileName: PYR4b.fastq
    offsets: [Using All]
    loadAllIndexes: [Not Using]
    compression: [Not Using]
    space: [Color Space]
    startReadNum: 1
    endReadNum: 2147483647
    keySize: [Not Using]
    maxKeyMatches: 8
    keyMissFraction: 1.000000
    maxNumMatches: 384
    whichStrand: [Both Strands]
    numThreads: 1
    queueLength: 250000
    tmpDir: ./
    timing: [Not Using]
    ************************************************************
    Searching for main indexes...
    Found 10 index (10 total files).
    Not using secondary indexes.
    ************************************************************
    Reading in reference genome from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.brg.
    In total read 18 contigs for a total of 12163423 bases
    ************************************************************
    Reading PYR4b.fastq into a temp file.
    Will process 19816967 reads.
    ************************************************************
    Searching index file 1/10 (index #1, bin #1)...
    Reading index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.1.1.bif.
    Read index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.1.1.bif.
    Reads processed: 19816967
    Cleaning up index.
    Searching index file 1/10 (index #1, bin #1) complete...
    Found 14240487 matches.
    ************************************************************
    Searching index file 2/10 (index #2, bin #1)...
    Reading index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.2.1.bif.
    Read index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.2.1.bif.
    Reads processed: 19816967
    Cleaning up index.
    Searching index file 2/10 (index #2, bin #1) complete...
    Found 14554594 matches.
    ************************************************************
    Searching index file 3/10 (index #3, bin #1)...
    Reading index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.3.1.bif.
    Read index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.3.1.bif.
    Reads processed: 19816967
    Cleaning up index.
    Searching index file 3/10 (index #3, bin #1) complete...
    Found 14101690 matches.
    ************************************************************
    Searching index file 4/10 (index #4, bin #1)...
    Reading index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.4.1.bif.
    Read index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.4.1.bif.
    Reads processed: 19816967
    Cleaning up index.
    Searching index file 4/10 (index #4, bin #1) complete...
    Found 13814082 matches.
    ************************************************************
    Searching index file 5/10 (index #5, bin #1)...
    Reading index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.5.1.bif.
    Read index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.5.1.bif.
    Reads processed: 19816967
    Cleaning up index.
    Searching index file 5/10 (index #5, bin #1) complete...
    Found 14599217 matches.
    ************************************************************
    Searching index file 6/10 (index #6, bin #1)...
    Reading index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.6.1.bif.
    Read index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.6.1.bif.
    Reads processed: 19816967
    Cleaning up index.
    Searching index file 6/10 (index #6, bin #1) complete...
    Found 13805101 matches.
    ************************************************************
    Searching index file 7/10 (index #7, bin #1)...
    Reading index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.7.1.bif.
    Read index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.7.1.bif.
    Reads processed: 19816967
    Cleaning up index.
    Searching index file 7/10 (index #7, bin #1) complete...
    Found 14758412 matches.
    ************************************************************
    Searching index file 8/10 (index #8, bin #1)...
    Reading index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.8.1.bif.
    Read index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.8.1.bif.
    Reads processed: 19816967
    Cleaning up index.
    Searching index file 8/10 (index #8, bin #1) complete...
    Found 14517528 matches.
    ************************************************************
    Searching index file 9/10 (index #9, bin #1)...
    Reading index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.9.1.bif.
    Read index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.9.1.bif.
    Reads processed: 19816967
    Cleaning up index.
    Searching index file 9/10 (index #9, bin #1) complete...
    Found 13907379 matches.
    ************************************************************
    Searching index file 10/10 (index #10, bin #1)...
    Reading index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.10.1.bif.
    Read index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.10.1.bif.
    Reads processed: 19816967
    Cleaning up index.
    Searching index file 10/10 (index #10, bin #1) complete...
    Found 13016565 matches.
    ************************************************************
    Merging the output from each index...
    [19816967]... completed.
    Found matches for 16501187 reads.
    Searching main indexes complete.
    ************************************************************
    ************************************************************
    In total, found matches for 16501187 out of 19816967 reads.
    ************************************************************
    Terminating successfully!
    Tags: None
    • jfk
      Junior Member
      • Jul 2011
      • 5
      #2
      Problem solved.

      The windows carriage return creeping into my script... was using notepad++ on my linux desktop.

      .. lesson: use vim/gedit!

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