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  • zhanxw
    Junior Member
    • Jun 2009
    • 7
    #1

    BFAST index, not understand warnings

    Hello,

    I want to created index files in color space from NCBI build 36 in color space.
    Here is my command
    `which time` bfast index -f NCBI36.fa -n 8 -w 14 -i 1 -A 1 -m 1111111111111111111111

    Then I got warning like "startContig was less than zero.", "endContig was greater than the number of contigs in the reference genome.". But I am sure I am using the same FASTA reference genome file. So is there anything I should do for these warnings? And is anyone have experience about how long it takes to build this index file?

    Part of the outputs:
    ------------------------------------------------------
    Checking input parameters supplied by the user ...
    Validating fastaFileName NCBI36.fa.
    Validating tmpDir path ./.
    Input arguments look good!
    ************************************************************
    ************************************************************
    Printing Program Parameters:
    programMode: [ExecuteProgram]
    fastaFileName: NCBI36.fa
    space: [Color Space]
    mask: 1111111111111111111111
    depth: 0
    hashWidth: 14
    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 NCBI36.fa.cs.brg.
    In total read 23 contigs for a total of 3022646526 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=23 and position=154913754.
    ************************************************************
    Currently on [contig,pos]:
    [-------4,---27000000]

    ------------------------------------------------------
    Tags: None
  • nilshomer
    Nils Homer
    • Nov 2008
    • 1283
    #2
    Originally posted by zhanxw View Post
    Hello,

    I want to created index files in color space from NCBI build 36 in color space.
    Here is my command
    `which time` bfast index -f NCBI36.fa -n 8 -w 14 -i 1 -A 1 -m 1111111111111111111111

    Then I got warning like "startContig was less than zero.", "endContig was greater than the number of contigs in the reference genome.". But I am sure I am using the same FASTA reference genome file. So is there anything I should do for these warnings? And is anyone have experience about how long it takes to build this index file?

    Part of the outputs:
    ------------------------------------------------------
    Checking input parameters supplied by the user ...
    Validating fastaFileName NCBI36.fa.
    Validating tmpDir path ./.
    Input arguments look good!
    ************************************************************
    ************************************************************
    Printing Program Parameters:
    programMode: [ExecuteProgram]
    fastaFileName: NCBI36.fa
    space: [Color Space]
    mask: 1111111111111111111111
    depth: 0
    hashWidth: 14
    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 NCBI36.fa.cs.brg.
    In total read 23 contigs for a total of 3022646526 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=23 and position=154913754.
    ************************************************************
    Currently on [contig,pos]:
    [-------4,---27000000]

    ------------------------------------------------------
    You can ignore the warnings if you didn't specify the "-s" or "-e" options. Each index takes about 4-5 hours to build (8 threads).

    Comment

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