[Bio-Linux] Problems with Tophat

[Sejal Modha]

Hi There,
I was facing similar issues with Bio-Linux version of  Tophat2 earlier this week.
Tophat-reports was giving errors when the multi-threading parameter -p was specified by the user, and my version of BioLinux8 was running the latest version of Tophat2 (2.0.13).
I fixed it by downloading the latest executables from Tophat2 website and it didn’t throw any errors with multi-threading.
http://ccb.jhu.edu/software/tophat/index.shtml

Sej
On 26 Jan 2015, at 16:06, Suzanne Gomes <suzanneluziagomes at gmail.com<mailto:suzanneluziagomes at gmail.com>> wrote:

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

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

Any suggestions for resolving these issues would be really appreciated.
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