[Bio-Linux] Problems with Tophat

[Suzanne Gomes]

Hi!

 

Brand new biolinux user here, and not really a computer person. My lab recently got a machine running biolinux 8 so we could do analysis with Galaxy. However I am having problems running Tophat and Tophat2. 

 

The first issue is with Tophat2, which gives the following error message:

 

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:    1.0.1.0

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

          Samtools version:    0.1.19.0

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

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

 

I read something in the mailing list from December that mentioned a problem with Tophat and bowtie not interacting properly, but it sounded as if that had been resolved. However, I think the install of biolinux on our computer was from before that fix (we had the install on a memory stick for a while before the computer was actually ready to go). But I am under the impression that biolinux automatically updates, so the fix should have been implemented after we installed, right? I’m not sure how to check if updates are installing.

 

The second issue is with Tophat (which I tried after Tophat2 failed), which gives this error message:

 

Error in tophat:

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

    for detailed help see http://tophat.cbcb.umd.edu/manual.html <http://tophat.cbcb.umd.edu/manual.html>
 

This error happens both with closure search turned on and turned off. 



Any suggestions for resolving these issues would be really appreciated.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.bioinformatics.org/pipermail/bio-linux-list/attachments/20150126/e5dc01d6/attachment.html>