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)
whereas
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 ?
sys.exit(main())
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
check_bowtie_index(idx_prefix)
File "/usr/bin/tophat", line 295, in check_bowtie_index
exit(1)
TypeError: 'str' object is not callable
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