[Bio-Linux] Biolinux7_Galaxy_Tophat_error

[Miskey, Csaba]

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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