Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Tophat: Warning: Encountered reference sequence with only gaps

    Hi,
    I have encountered one problem listed as follows. The results are not influenced by this Warning. But I don't know if there are other influences. Could any one can tell me? Thanks.
    -------------------
    [Sun Feb 13 20:07:48 2011] Beginning TopHat run (v1.0.12)
    -----------------------------------------------
    [Sun Feb 13 20:07:48 2011] Preparing output location /home/pengchy/tophat/tophat_out/SC_b_16h/part2/
    [Sun Feb 13 20:07:48 2011] Checking for Bowtie index files
    [Sun Feb 13 20:07:48 2011] Checking for reference FASTA file
    [Sun Feb 13 20:07:48 2011] Checking for Bowtie
    Bowtie version: 0.12.5.0
    [Sun Feb 13 20:07:49 2011] Checking reads
    seed length: 90bp
    format: fastq
    quality scale: --solexa1.3-quals
    [Sun Feb 13 21:06:26 2011] Mapping reads against test.scafSeq.fill_FG.2 with Bowtie
    [Mon Feb 14 00:10:41 2011] Joining segment hits
    Splitting reads into 3 segments
    [Mon Feb 14 00:50:45 2011] Mapping reads against test.scafSeq.fill_FG.2 with Bowtie
    [Mon Feb 14 06:03:03 2011] Mapping reads against test.scafSeq.fill_FG.2 with Bowtie
    [Mon Feb 14 10:37:23 2011] Mapping reads against test.scafSeq.fill_FG.2 with Bowtie
    [Mon Feb 14 15:21:41 2011] Mapping reads against test.scafSeq.fill_FG.2 with Bowtie
    [Mon Feb 14 18:12:48 2011] Joining segment hits
    Splitting reads into 3 segments
    [Mon Feb 14 18:37:11 2011] Mapping reads against test.scafSeq.fill_FG.2 with Bowtie
    [Mon Feb 14 22:54:31 2011] Mapping reads against test.scafSeq.fill_FG.2 with Bowtie
    [Tue Feb 15 03:32:22 2011] Mapping reads against test.scafSeq.fill_FG.2 with Bowtie
    [Tue Feb 15 07:34:35 2011] Searching for junctions via segment mapping
    [Tue Feb 15 09:11:17 2011] Retrieving sequences for splices
    [Tue Feb 15 09:16:18 2011] Indexing splices
    Warning: Encountered reference sequence with only gaps
    Warning: Encountered reference sequence with only gaps
    Warning: Encountered reference sequence with only gaps

  • #2
    Hi pengchy,

    Try to upgrade to the latest versions of Bowtie and Tophat. In particular Bowtie <0.12.7 seem to have issues with all-gap sequence (see http://bowtie-bio.sourceforge.net/index.shtml).

    Having said this, I'm also finding the warning "Warning: Encountered reference sequence with only gaps" and I'm using the latest versions. Curiously, I get the warnings when I align 57 bp reads but no warnings with 35 bp reads.

    so I'm also interested in knowing why this warnings occur and if they affect the results.

    Here's my tophat log file:

    Code:
    [Wed Feb  2 22:48:13 2011] Beginning TopHat run (v1.2.0)
    -----------------------------------------------
    [Wed Feb  2 22:48:13 2011] Preparing output location .//
    [Wed Feb  2 22:48:13 2011] Checking for Bowtie index files
    [Wed Feb  2 22:48:13 2011] Checking for reference FASTA file
    [Wed Feb  2 22:48:13 2011] Checking for Bowtie
    	Bowtie version:			 0.12.7.0
    [Wed Feb  2 22:48:13 2011] Checking for Samtools
    	Samtools Version: 0.1.10
    [Wed Feb  2 22:48:39 2011] Checking reads
    	min read length: 57bp, max read length: 57bp
    	format:		 fastq
    	quality scale:	 phred64 (reads generated with GA pipeline version >= 1.3)
    [Wed Feb  2 22:58:53 2011] Reading known junctions from GTF file
    [Wed Feb  2 23:02:06 2011] Mapping reads against Sus_scrofa.Sscrofa9.56.dna.toplevel with Bowtie
    [Wed Feb  2 23:02:48 2011] Joining segment hits
    [Wed Feb  2 23:04:24 2011] Mapping reads against Sus_scrofa.Sscrofa9.56.dna.toplevel with Bowtie(1/2)
    [Wed Feb  2 23:05:06 2011] Mapping reads against Sus_scrofa.Sscrofa9.56.dna.toplevel with Bowtie(2/2)
    [Wed Feb  2 23:05:07 2011] Mapping reads against Sus_scrofa.Sscrofa9.56.dna.toplevel with Bowtie
    [Wed Feb  2 23:29:46 2011] Joining segment hits
    [Wed Feb  2 23:39:28 2011] Mapping reads against Sus_scrofa.Sscrofa9.56.dna.toplevel with Bowtie(1/2)
    [Thu Feb  3 00:20:46 2011] Mapping reads against Sus_scrofa.Sscrofa9.56.dna.toplevel with Bowtie(2/2)
    [Thu Feb  3 00:35:59 2011] Searching for junctions via segment mapping
    [Thu Feb  3 01:08:43 2011] Retrieving sequences for splices
    [Thu Feb  3 01:13:58 2011] Indexing splices
    Warning: Encountered reference sequence with only gaps
    Warning: Encountered reference sequence with only gaps
    [Thu Feb  3 01:24:18 2011] Mapping reads against segment_juncs with Bowtie
    [Thu Feb  3 01:37:24 2011] Mapping reads against segment_juncs with Bowtie
    [Thu Feb  3 01:50:42 2011] Joining segment hits
    [Thu Feb  3 01:52:55 2011] Mapping reads against segment_juncs with Bowtie
    [Thu Feb  3 02:24:13 2011] Mapping reads against segment_juncs with Bowtie
    [Thu Feb  3 02:46:52 2011] Joining segment hits
    [Thu Feb  3 02:57:11 2011] Reporting output tracks
    -----------------------------------------------
    Run complete [04:31:14 elapsed]
    All the best

    Dario

    Comment


    • #3
      Originally posted by dariober View Post
      Hi pengchy,

      Try to upgrade to the latest versions of Bowtie and Tophat. In particular Bowtie <0.12.7 seem to have issues with all-gap sequence (see http://bowtie-bio.sourceforge.net/index.shtml).

      Having said this, I'm also finding the warning "Warning: Encountered reference sequence with only gaps" and I'm using the latest versions. Curiously, I get the warnings when I align 57 bp reads but no warnings with 35 bp reads.
      Yes, as you say, the warning still output when we upgrade the bowtie to version 0.12.7.

      Comment


      • #4
        Originally posted by pengchy View Post
        Warning: Encountered reference sequence with only gaps
        Warning: Encountered reference sequence with only gaps
        Warning: Encountered reference sequence with only gaps
        I see this when my input Fasta has only Ns
        Homepage: Dan Bolser
        MetaBase the database of biological databases.

        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
        51 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