[Bio-Linux] Biolinux7_Galaxy_Tophat_error

Tim Booth tbooth at ceh.ac.uk
Fri Sep 6 12:34:13 EDT 2013


Hi,

OK, thanks for the info.  I must say, I find Galaxy quite confusing when
working out which data needs to be fed to which programs.  I always tend
to use the command line as it's faster and there is one less layer of
complexity.

Bio-Linux comes with Tophat which is actually Tophat2 (2.0.9 as you saw
below) and it doesn't matter if you run tophat or tophat2 as they are
both the same program.  But bowtie and bowtie2 are separate programs,
installed as separate packages.  You can find out what programs these
packages provide like so:

tbooth at balisaur[tbooth]dpkg -L bowtie | grep /usr/bin.
/usr/bin/bowtie-build-debug
/usr/bin/bowtie-build
/usr/bin/bowtie-inspect
/usr/bin/bowtie
/usr/bin/bowtie-debug
/usr/bin/bowtie-inspect-debug

tbooth at balisaur[tbooth]dpkg -L bowtie2 | grep /usr/bin.
/usr/bin/bowtie2-align
/usr/bin/bowtie2-inspect
/usr/bin/bowtie2
/usr/bin/bowtie2-build
/usr/bin/bowtie2-inspect-debug
/usr/bin/bowtie2-build-debug
/usr/bin/bowtie2-align-debug

I'm not sure what's up with the index files, but I'm hoping that
re-indexing your genome with bowtie2-build (not bowtie-build) will solve
the problem.  Any joy with that?

Cheers,

TIM

On Fri, 2013-09-06 at 16:48 +0100, Miskey, Csaba wrote:
> Hi Tim,
> 
> Thanks for your reply!
> 
> The error msg. I got in Galaxy:
> 0 bytes
> An error occurred running this job: TopHat v2.0.9
> TopHat v2.0.9
> tophat -p 4 /var/lib/galaxy-server/genomes/hg19/bowtie/base/hg19 /usr/lib/galaxy-server/database/files/000/dataset_80.dat
> Error in tophat:
> 
> [2013-09-05 19:54:18] Beginning TopHat run (v2.0.9)
> 
> But then I might see the problem.
> In Galaxy there are two tools to choose from <Tophat for Illumina> and <Tophat2>. Both of them however call TopHat2!
> And Tophat2 uses different indexes from Tophat (old). As they say in the galaxy wiki:
> < Bowtie and Tophat use the same index set, and Bowtie2 and Tophat2 use the same index set, but Bowtie/Tophat and Bowtie2/Tophat2 do not use the same index set.>
> So I thought that by clicking the <Tophat for Illumina> tool I'd fine with my Bowtie indexes. I do not have indexes for Bowtie2!
> So my Bowtie works fine but since <Tophat for Illumina> calls Tophat2 it does not find indexes for running.
> Right?
> 
> Would    sudo  bowtie-build -f hg19.fa hg19   solve the problem? (found in: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup)
> (I do not have admin rights, and grasping  Linux is yet to accomplish too, hah! )
> 
> My Bowtie2 version:
> 
> bowtie2 --version               
> /usr/bin/bowtie2-align version 2.1.0
> 64-bit
> Built on wani09
> Tue Apr 30 09:03:44 UTC 2013
> Compiler: gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5) 
> Options: -O3 -m64 -msse2 -funroll-loops -g3 
> Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
> 
> Many thanks again!
> 
> Cheers,
> 
> Csaba
> 
> -----Original Message-----
> From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Tim Booth
> Sent: Freitag, 6. September 2013 16:35
> To: bio-linux at nebclists.nerc.ac.uk
> Subject: Re: [Bio-Linux] Biolinux7_Galaxy_Tophat_error
> 
> Hi Csaba,
> 
> Welcome to the Bio-Linux list.  You say that Tophat is giving you an error but you've not told us what the error message actually says, so it's hard to guess what the problem might be.
> 
> I've tested Tophat on the standard test data that they provide, both running via Galaxy and on the command line, and both seem to work, but I've not done any more extensive testing or used the software in anger.
> My impression is that Tophat in Galaxy always uses Bowtie2 (they don't expose the option to select Bowtie1) so I don't think this can be related to Jeremy's problem.  If you open a terminal and type:
> 
> bowtie2 --version
> 
> What do you get?
> 
> Cheers,
> 
> TIM
> 
> On Fri, 2013-09-06 at 13:24 +0100, Miskey, Csaba wrote:
> > Dear Guys,
> > 
> >  
> > 
> > I wonder if Jeremy’s problem with Tophat (error when trying to run it) 
> > was solved by updating to 2.0.9.
> > 
> > My Galaxy running under Biolinux7 has Tophat 2.0.9. and I still cannot 
> > make it run. (Bowtie accepts and runs ok with the same fastqsanger 
> > file with which Tophat throws the error. Though, as I figured the two 
> > mappers take the same set of indexes).
> > 
> >  
> > 
> > Any help would be greatly appreciated!
> > 
> >  
> 
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-- 
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://nebc.nerc.ac.uk
+44 1491 69 2705



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