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Old 06-02-2010, 05:00 AM   #3
Location: India

Join Date: Jun 2010
Posts: 20

To raela,

I had placed all the following requisite executables in root '/usr/bin'

1. bowtie
2. bowtie-inspect
3. bowtie-build
4. tophat

My input files : reads_1.fq, reads_2.fq
are in Path: /home/user1/NGS/TopHat_Test_data/test_data)
My Bowtie index files are in Path: /home/user2/bowtie_install/bowtie-0.12.3/indexes/

Note: user1 doesn't have permission to directly access the user2 directory where the Bowtie 'indexes' sub directory is except through login as the admin.

I am running the command

tophat -r 20 test_ref reads_1.fq reads_2.fq

from the directory: /home/user1/NGS/TopHat_Test_data/test_data

I also tried running the same command as

tophat -r 20 /home/user2/bowtie_install/bowtie-0.12.3/indexes/test_ref reads_1.fq reads_2.fq

then i am getting the error as

-bash-3.1$ tophat -r 20 /home/user2/bowtie_install/bowtie-0.12.3/indexes/test_ref reads_1.fq reads_2.fq

[Wed Jun 2 17:24:16 2010] Beginning TopHat run (v1.0.7)
[Wed Jun 2 17:24:16 2010] Preparing output location ./tophat_out/
[Wed Jun 2 17:24:16 2010] Checking for Bowtie index files
Error: Could not find Bowtie index files /home/user2/bowtie_install/bowtie-0.12.3/indexes/test_ref.*
Traceback (most recent call last):
File "/usr/bin/tophat", line 1476, in ?
File "/usr/bin/tophat", line 1411, in main
(ref_fasta, idx_bfa) = check_index(bwt_idx_prefix)
File "/usr/bin/tophat", line 378, in check_index
File "/usr/bin/tophat", line 295, in check_bowtie_index
TypeError: 'str' object is not callable
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