Question: Problems with Tophat/Tophat2 on local server
gravatar for Suzanne Gomes
3.9 years ago by
Suzanne Gomes120
Suzanne Gomes120 wrote:

I'm having problems running Tophat on my local galaxy instance (I'm running it via biolinux 8). 

Initially I tried running Tophat2, but got the following error:


Fatal error: Tool execution failed

Building a SMALL index


[2015-01-19 12:10:58] Beginning TopHat run (v2.0.9)


[2015-01-19 12:10:58] Checking for Bowtie

  Bowtie 2 not found, checking for older version..

          Bowtie version:

[2015-01-19 12:10:58] Checking for Samtools

        Samtools version:

[2015-01-19 12:10:58] Checking for Bowtie index files (genome)..

Error: Could not find Bowtie index files (genome.*.ebwt)


I was under the impression that bowtie would create the index itself from the provided genome (which was a Drosophila genome from Flybase, lexicographically sorted).

Then I tried running Tophat instead, wondering if I'd get the same error. Instead, I got an error regarding the closure search (I tried running it with closure search turned on and off and both times got an error):


Error in tophat:

tophat: option --no-closure-search not recognized

    for detailed help see


Any ideas on what would be causing these errors? This is a newly set up machine, so this is the first time Tophat's being run on this computer. 


PS. Is there a way to set up bug reporting on a local galaxy instance?







rna-seq • 1.9k views
ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by Suzanne Gomes120
gravatar for Jennifer Hillman Jackson
3.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The indexes created by Bowtie2 are the ones needed for Tophat2. Try installing that tool and see if the Custom Genome index creation works.

The other option is to create the indexes natively using Data Managers. You can install Bowtie2 and the DM from the tool shed.

Also watch for paths. When Tophat2 and Bowtie2 install, symlinks are created that rename these to just Tophat/Bowtie in the paths. Double checking that these are removed is a good idea, some of your output makes me think that this may be the case (with Bowtie2 actually installed already).

Hopefully this helps toward a solution, Jen, Galaxy team

ADD COMMENTlink written 3.9 years ago by Jennifer Hillman Jackson25k
gravatar for Suzanne Gomes
3.9 years ago by
Suzanne Gomes120
Suzanne Gomes120 wrote:

Hi Jennifer,

I tried installing Bowtie 2 from the toolshed, but wasn't sure which of the listed files to download. So I downloaded 'package_bowtie_2_2_4', which was successful. I then tried to rerun Tophat2, but got the same error message as before. So I went back into the Toolshed and tried to download 'bowtie2', but got the message 'Internal server error', with a suggestion that reloading the page might help (it didn't). 

So my questions are...

a) Am I downloading the right file?

b) Why am I getting the internal server error? I actually got the same error when trying to install FastQC, but was able to install Trimmomatic with no problem. I'm wondering if it's a case of tools with repository dependencies not working for some reason? 

Thanks for your help


ADD COMMENTlink written 3.9 years ago by Suzanne Gomes120
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