TOPHAT / TOPHAT2 checking bowtie version error?

[jmt]

Hi all,

I downloaded the Linux binary version of the latest version of Tophat as well as the latest Linux binary version of Bowtie2, and I get the following error when I try to execute a simple "tophat2 index fastq1 fastq2" command (no options or anything). I get the following error. Anyone have a clue what this is about?


[2012-11-02 09:34:10] Beginning TopHat run (v2.0.5)
-----------------------------------------------
[2012-11-02 09:34:10] Checking for Bowtie
Traceback (most recent call last):
File "/gpfs/fs121/h/toung/downloads/tophat-2.0.5.Linux_x86_64/tophat", line 4035, in <module>
sys.exit(main())
File "/gpfs/fs121/h/toung/downloads/tophat-2.0.5.Linux_x86_64/tophat", line 3836, in main
check_bowtie(params)
File "/gpfs/fs121/h/toung/downloads/tophat-2.0.5.Linux_x86_64/tophat", line 1473, in check_bowtie
bowtie_version = get_bowtie_version(params.bowtie2)
File "/gpfs/fs121/h/toung/downloads/tophat-2.0.5.Linux_x86_64/tophat", line 1351, in get_bowtie_version
bowtie_version = [int(x) for x in ver_numbers[:3]] + [int(ver_numbers[3][4:])]
IndexError: list index out of range





**** FYI, here are the versions I'm using


$ bowtie2 --version
/gpfs/fs121/h/toung/bin/bowtie2-align version 2.0.2
64-bit
Built on ********
Fri Nov 2 09:27:25 EDT 2012
Compiler: gcc version 4.4.6 20120305 (Red Hat 4.4.6-4) (GCC)
Options: -O3 -m64 -msse2 -funroll-loops -g3
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}


$ ./tophat2 --version
TopHat v2.0.5

[westerman]

Yeap. Same here. My sysadmin changed bowtie2 out from under me over night and I spent some frustrating time yesterday morning tracking down the problem. He basically shrugged his shoulders and told me to use the previous version of bowtie2. :-( Ok, I can see that incompatibility between Tophat and bowtie2 is not his problem but ... still ... I wanted more sympathy.

[RocheKermit]

Yep! Same problem there. I've found you're post, switched back to bowtie 2.0.0.7 (a secret agent number, no?) and it's now ok.
Shall I ask you haw have you been aware that TopHat 2 is not compatible with bowtie 2.0.2?

[nhry]

I had the same issue when using tophat 2.0.5. I fixed it by running with the --bowtie1 option. Alternatively, like RocheKermit and westerman have said, you can downgrade your bowtie2 version to the beta 2.0.0.7 for it to work.
There is also a new version of tophat2 (2.0.6, released 3 days ago) which fixes this bug and a few other bugs as well. When using this version I was able to get it working with bowtie2 version 2.0.2