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Old 12-08-2010, 12:02 PM   #1
Location: Cambridge, MA

Join Date: Jan 2010
Posts: 27
Default Tophat v1.1.4 bug - cannot handle non-numeric versions of Samtools


I was just using the new version of Tophat with Samtools-0.1.12a and got the following error:

[Wed Dec 8 16:56:42 2010] Beginning TopHat run (v1.1.4)
[Wed Dec 8 16:56:42 2010] Preparing output location ./tophat_out/
[Wed Dec 8 16:56:42 2010] Checking for Bowtie index files
[Wed Dec 8 16:56:42 2010] Checking for reference FASTA file
[Wed Dec 8 16:56:42 2010] Checking for Bowtie
Bowtie version:
[Wed Dec 8 16:56:42 2010] Checking for Samtools
Traceback (most recent call last):
File "/share/apps/alignment/tophat/default/bin/tophat", line 2223, in ?
File "/share/apps/alignment/tophat/default/bin/tophat", line 2136, in main
File "/share/apps/alignment/tophat/default/bin/tophat", line 877, in check_samtools
samtools_version = get_samtools_version()
File "/share/apps/alignment/tophat/default/bin/tophat", line 864, in get_samtools_version
samtools_version = [int(x.split('-')[0]) for x in version_val.split('.')]
ValueError: invalid literal for int(): 12a

Tophat v1.1.4 does work with the previous version of Samtools (Samtools-0.1.11).

Hopefully this bug will be solved.
adumitri is offline   Reply With Quote
Old 12-29-2010, 02:58 PM   #2
Location: Toronto

Join Date: Nov 2009
Posts: 24

Yes, I am having the same problem after upgrading to "samtools-0.1.12a". I guess it should be an easy fix, just hope the TopHat guys can find time to do it soon (or if the samtools guys can stick to the old convention). Thanks!
HTS is offline   Reply With Quote
Old 12-30-2010, 11:07 AM   #3
Junior Member
Location: San Francisco, CA

Join Date: Sep 2009
Posts: 8
Default Comment out check samtools in tophat script

I ran into this problem and I just commented the relevant lines out in the get_samtools_version() and check_samtools() functions of the tophat script and it seems to work fine now.
elizzybethy is offline   Reply With Quote
Old 01-05-2011, 09:09 AM   #4
Location: SF Bay Area

Join Date: Aug 2008
Posts: 16

i just edited the version number in bamtk.c in the samtools folder to 1.12 and did a:

make clean


and we seem to be all set.
seqfast is offline   Reply With Quote
Old 01-10-2011, 06:18 AM   #5
Location: College Park

Join Date: Oct 2010
Posts: 27

Hi guys,

I fixed this problem, and we will release TopHat 1.2.0 soon!
Daehwan is offline   Reply With Quote

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