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Old 11-10-2014, 05:46 AM   #1
bsmith030465
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Default tophat2 : Bowtie2 not found...

Hi,

I am new to NGS analysis. I was trying to follow a protocol for an analysis that calls on tophat2 on a cluster. After looking at some previous posts on this forum, I am trying to specify the absolute path. The code I execute is:

% tophat2 -p 8 -o S1_R1_out -G /home/bs/mm10/Genes/genes.gtf /home/bs/mm10/Sequence/Bowtie2Index/genome S1_R1_1.fastq S1_R1_2.fastq

However, I get the following error message:

==========================
[2014-11-10 09:26:35] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2014-11-10 09:26:35] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Error: Bowtie not found on this system.

==========================

I checked and bowtie2 is in my path:

% bowtie2
No index, query, or output file specified!
Bowtie 2 version 2.2.3 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage:
bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]


What am I doing wrong?

thanks!
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Old 11-10-2014, 07:01 AM   #2
GenoMax
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What job scheduler are you using on the cluster? Are the jobs running as "you" (whatever account that you posted the results from above)?
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Old 11-10-2014, 08:33 AM   #3
bsmith030465
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Hi max,

I am running in an interactive mode - I am executing the commands on one of the nodes. All executable are in /Usr/local/bin, and they (tophat2 & bowtie2) appear to be accessible...
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Old 11-10-2014, 08:38 AM   #4
GenoMax
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I think you are using an old version of TopHat (v.2.0.6) that is likely incompatible with your current bowtie2 (which appears to be of a more recent vintage). You may need to get the admins to upgrade TopHat to latest.
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Old 11-10-2014, 10:28 AM   #5
blakeoft
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Can you download the latest versions of tophat and bowtie2 to your home directory? That would be a pretty easy fix, and you'd have the latest version of the software too.
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Old 11-10-2014, 10:28 AM   #6
blancha
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Yes, GenoMax is correct.
Update to TopHat 2.0.13 yourself or ask the system administrators to do it for your.
This issue was fixed in TopHat 2.0.12, as indicated on the TopHat website.

#####

TopHat 2.0.12 release 6/24/2014
Version 2.0.12 is a maintenance release with the following simple fix:

This version is compatible with Bowtie2 v2.2.3.
http://ccb.jhu.edu/software/tophat/index.shtml
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