[Bio-Linux] Problems with Tophat

[Tim Booth]

Hi Suzanne,

The first thing to note is that Tophat and Tophat2 are actually the same
program.
(Unlike Bowtie and Bowtie2 which are different)

The second thing I noticed is you have Tophat 2.0.9 so this is
definitely out-of-date.  To check and install updates ensure you are
logged in as a user with "sudo" privileges and then start the Software
Updater.  To find that, click on the swirly icon at the top left of your
screen and then type "update" into the search box.  This should bring up
the relevant icon and guide you through the rest.

If you are only running in the terminal, or if the graphical updater
gives you errors, then you can do it this way:

$ sudo apt-get update
$ sudo apt-get dist-upgrade

Let me know if that works/helps.

In general, we can't do fully transparent updates of all software so you
do need to check every so often and accept new updates.

Cheers,

TIM

On Mon, 2015-01-26 at 16:06 +0000, Suzanne Gomes 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.
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297