Does anyone know what this output in tophat mean? How much of a problem is it?
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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:
[Sun Aug 08 23:20:23 2010] Beginning TopHat run (v1.0.14)
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[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]
-steve
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Originally posted by digitonin View PostI never did find an answer to this. I didn't see any problems associated it with it either though.
First of all, sorry for bumping such a old post, but this problem still persists...
Does anyone found a reason why does this happens?
I have obtained this same warning message when using the current Drosophila melanogaster reference (r6.03; BDGP5.78)
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Hi,
I am using bowtie 1.1.2 and I get the same message -
encountered reference sequence with gaps
My genome is not repmasked and has the following type of header
>ta_IWGSC_CSSassembly_1as_v2_44039
Does such a warning interfere with the bowtie-build in anyway?
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This will happen whenever you have cases like this
Code:>chr1 >chr2 ACAGCTACT
Code:>chr3 NNNNNNN >chr4 ACGTAGCTGACT
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