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Old 08-05-2010, 04:59 PM   #1
digitonin
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Default Warning: Encountered reference sequence with only gaps

Does anyone know what this output in tophat mean? How much of a problem is it?
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Old 08-08-2010, 10:52 PM   #2
scozza
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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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Old 04-19-2012, 02:29 PM   #3
ataheri
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Did you find the answer to this warning message? I have similar problem with my data as well and appreciate if you can let me know how to deal with it.
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Old 04-19-2012, 02:58 PM   #4
digitonin
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I never did find an answer to this. I didn't see any problems associated it with it either though.
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Old 10-19-2012, 08:43 AM   #5
DunderChief
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Default

-------bump-------

I also get this using Ensembl human reference (v. 68)
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Old 10-19-2012, 09:29 AM   #6
Wallysb01
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Is it because you are using a repeat masked genome and possibly some of the sequences have been completely masked? I've seen this in other, less complete genomes, so I'm unsure if this would be the case with the human genome.
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Old 10-19-2012, 10:20 AM   #7
DunderChief
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Thanks Wallysb01, that's propably it. I am using a soft-masked reference (low complexity regions are lowercase).
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Old 05-31-2013, 06:23 AM   #8
Tuinhof
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Default

I also have the same error message, when I use the Homo_sapiens.GRCh37.71.dna.toplevel reference.
Does this upper/lower case issue influence the mapping/counting outcome?
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Old 10-10-2013, 07:46 PM   #9
xfh
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I also have the same warning message with Homo_sapiens.GRCh37.71.dna.toplevel reference. anyone can explain it?
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Old 01-20-2015, 01:06 AM   #10
Hugo A F Santos
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Quote:
Originally Posted by digitonin View Post
I never did find an answer to this. I didn't see any problems associated it with it either though.
-----------BUMP-----------

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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Old 01-20-2015, 01:35 AM   #11
digitonin
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Hugo,

This probably has to do with the lowercase or the use of N's in the reference. Either way, it is not a problem.
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Old 03-09-2016, 05:59 PM   #12
Sow
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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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Old 03-10-2016, 01:18 AM   #13
dpryan
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Default

This will happen whenever you have cases like this
Code:
>chr1
>chr2
ACAGCTACT
or this

Code:
>chr3
NNNNNNN
>chr4
ACGTAGCTGACT
It's just a warning, which means that there won't be an issue with index creation, but you should really fix your fasta files.
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