Tophat: Warning: Encountered reference sequence with only gaps

[pengchy]

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

[dariober]

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:

[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

[pengchy]

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.

[dan]

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