Tweet
Does anyone know what this output in tophat mean? How much of a problem is it?
-
-
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:
Should we be concerned?[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]
-steve -
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.Comment
-
I never did find an answer to this. I didn't see any problems associated it with it either though.Comment
-
-------bump-------
I also get this using Ensembl human reference (v. 68)Comment
-
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.Comment
-
Thanks Wallysb01, that's propably it. I am using a soft-masked reference (low complexity regions are lowercase).Comment
-
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?Comment
-
I also have the same warning message with Homo_sapiens.GRCh37.71.dna.toplevel reference. anyone can explain it?Comment
-
-----------BUMP-----------Originally posted by digitonin View Post
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)Comment
-
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.Comment
-
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?Comment
-
This will happen whenever you have cases like this
or thisCode:>chr1 >chr2 ACAGCTACT
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.Code:>chr3 NNNNNNN >chr4 ACGTAGCTGACT
Comment
-
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM -
Studying ecosystems means dealing with complex, multi-species communities that are hard to observe at scale. This complexity, however, hides many important questions to be answered, from how biogeochemical cycles work and how climate change can affect species distribution to how conservation strategies can work best.
Genomics, particularly since the expansion of NGS, has transformed ecosystem ecology. By sequencing environmental DNA, we can now assess biodiversity without direct...05-06-2026, 09:04 AM
Comment