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Old 08-08-2010, 09:52 PM   #2
scozza
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Location: Colorado

Join Date: Jan 2009
Posts: 16
Default I am curious too...

I am curious as well as to what this truly means and if it should be a concern. I encountered it on my latest runs in which I am using the Ensembl version of the human genome assembly. An example of the warning displayed is:

Quote:
[Sun Aug 08 23:20:23 2010] Beginning TopHat run (v1.0.14)
-----------------------------------------------
[Sun Aug 08 23:20:23 2010] Preparing output location brain/
[Sun Aug 08 23:20:23 2010] Checking for Bowtie index files
[Sun Aug 08 23:20:23 2010] Checking for reference FASTA file
[Sun Aug 08 23:20:23 2010] Checking for Bowtie
Bowtie version: 0.12.5.0
[Sun Aug 08 23:20:23 2010] Checking reads
seed length: 36bp
format: fastq
quality scale: phred33 (default)
[Sun Aug 08 23:23:07 2010] Mapping reads against Homo_sapiens.GRCh37.59 with Bowtie
[Sun Aug 08 23:26:43 2010] Joining segment hits
[Sun Aug 08 23:27:09 2010] Mapping reads against Homo_sapiens.GRCh37.59 with Bowtie
[Sun Aug 08 23:31:02 2010] Joining segment hits
[Sun Aug 08 23:31:26 2010] Searching for junctions via segment mapping
[Sun Aug 08 23:46:58 2010] Retrieving sequences for splices
[Sun Aug 08 23:52:48 2010] Indexing splices
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
[Sun Aug 08 23:54:58 2010] Mapping reads against segment_juncs with Bowtie
[Sun Aug 08 23:58:35 2010] Joining segment hits
[Sun Aug 08 23:59:00 2010] Mapping reads against segment_juncs with Bowtie
[Mon Aug 09 00:02:49 2010] Joining segment hits
[Mon Aug 09 00:03:13 2010] Reporting output tracks
-----------------------------------------------
Run complete [00:45:40 elapsed]
Should we be concerned?

-steve
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