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
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
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