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Old 02-15-2011, 01:45 AM   #2
dariober
Senior Member
 
Location: Cambridge, UK

Join Date: May 2010
Posts: 311
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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
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