Tophat v1.1.4 bug - cannot handle non-numeric versions of Samtools

adumitri · 12-08-2010, 12:02 PM

Hi,

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: 0.12.7.0
[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 ?
sys.exit(main())
File "/share/apps/alignment/tophat/default/bin/tophat", line 2136, in main
check_samtools()
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.
Alexandra

HTS · 12-29-2010, 02:58 PM

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!

elizzybethy · 12-30-2010, 11:07 AM

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.

seqfast · 01-05-2011, 09:09 AM

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

make clean

make

and we seem to be all set.

Daehwan · 01-10-2011, 06:18 AM

Hi guys,

I fixed this problem, and we will release TopHat 1.2.0 soon!

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12-08-2010, 12:02 PM	#1
adumitri Member Location: Cambridge, MA Join Date: Jan 2010 Posts: 27	Tophat v1.1.4 bug - cannot handle non-numeric versions of Samtools Hi, 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: 0.12.7.0 [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 ? sys.exit(main()) File "/share/apps/alignment/tophat/default/bin/tophat", line 2136, in main check_samtools() 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. Alexandra

12-30-2010, 11:07 AM	#3
elizzybethy Junior Member Location: San Francisco, CA Join Date: Sep 2009 Posts: 8	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.

12-29-2010, 02:58 PM	#2
HTS Member 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!

01-05-2011, 09:09 AM	#4
seqfast Member 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 make and we seem to be all set.

01-10-2011, 06:18 AM	#5
Daehwan Member Location: College Park Join Date: Oct 2010 Posts: 27	Hi guys, I fixed this problem, and we will release TopHat 1.2.0 soon!