Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Any way to validate BFAST index file?

    Continuing my experiments with bfasta (see http://seqanswers.com/forums/showthr...0855#post50855 ), I've built an index for a specific mask. I am getting conflicting file sizes for the index file, though. My command to build the index is
    time bfast index -A 0 -f reference.fa \
    -i 1 -m 10011110101111101111101101101 -w 14 -R

    And among other info, the program reports "Index size is 8.007GB". However, a ls of the directory reports the file size as 6.5G. So I don't know if the entire file has been written to disk, or if b=fast is misreporting the size.

    Is there any tool that will validate whether my index file is complete and correct?

    Thanks

  • #2
    The index is compressed (with gzip) on disk, and so the index size reported is the size in memory. Use "bheader" to get info about the index.

    Comment


    • #3
      Originally posted by nilshomer View Post
      The index is compressed (with gzip) on disk, and so the index size reported is the size in memory. Use "bheader" to get info about the index.
      T h a n k s!

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Strategies for Sequencing Challenging Samples
        by seqadmin


        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
        03-22-2024, 06:39 AM
      • seqadmin
        Techniques and Challenges in Conservation Genomics
        by seqadmin



        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

        Avian Conservation
        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
        03-08-2024, 10:41 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 06:37 PM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      9 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      49 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      67 views
      0 likes
      Last Post seqadmin  
      Working...
      X