Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Time
  • Show
Clear All
new posts
Previous template Next
  • 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

        Previous template Next

        Latest Articles

        Collapse
        • SEQadmin2
          Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
          by SEQadmin2



          Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

          Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating          ...
          10-14-2026, 09:55 AM
        • SEQadmin2
          New Genomics Technologies Take Aim at Long-Standing Limits
          by SEQadmin2


          Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

          We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing          ...
          09-28-2026, 10:25 AM
        View All

        ad_right_rmr

        Collapse

        News

        Collapse
        Topics Statistics Last Post
        Exeter-Led Study Maps What an Average Human Genome Looks Like by SEQadmin2
        Started by SEQadmin2, 10-22-2026, 11:13 AM
        0 responses
        32 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-22-2026, 11:13 AM  
        Long-Read Sequencing Uncovers Cancer Mutations Conventional Testing Missed by SEQadmin2
        Started by SEQadmin2, 10-22-2026, 10:48 AM
        0 responses
        23 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-22-2026, 10:48 AM  
        Mayo Clinic-Led Study Detects DNA Mutations Across Noncancerous Tissues by SEQadmin2
        Started by SEQadmin2, 10-15-2026, 10:52 AM
        0 responses
        40 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-15-2026, 10:52 AM  
        Study Finds Chromatin Motion Holds Steady Until Cells Face Stress by SEQadmin2
        Started by SEQadmin2, 10-14-2026, 05:39 AM
        0 responses
        45 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-14-2026, 05:39 AM  
        View All
        Working...