populus@Rust:~/tophat-1.0.9/bin/test_data$ ../tophat -r 20 test_ref reads_1.fq reads_2.fq
[Wed Jul 22 04:03:11 2009] Beginning TopHat run (v1.0.9)
-----------------------------------------------
[Wed Jul 22 04:03:11 2009] Preparing output location ./tophat_out/
[Wed Jul 22 04:03:11 2009] Checking for Bowtie index files
[Wed Jul 22 04:03:11 2009] Checking for reference FASTA file
[Wed Jul 22 04:03:11 2009] Checking for Bowtie
Traceback (most recent call last):
File "../tophat", line 1484, in <module>
sys.exit(main())
File "../tophat", line 1420, in main
check_bowtie()
File "../tophat", line 567, in check_bowtie
bowtie_version = get_bowtie_version()
File "../tophat", line 548, in get_bowtie_version
proc = subprocess.Popen(['bowtie', '--version'],stdout=subprocess.PIPE)
File "/usr/lib/python2.5/subprocess.py", line 594, in __init__
errread, errwrite)
File "/usr/lib/python2.5/subprocess.py", line 1147, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
[Wed Jul 22 04:03:11 2009] Beginning TopHat run (v1.0.9)
-----------------------------------------------
[Wed Jul 22 04:03:11 2009] Preparing output location ./tophat_out/
[Wed Jul 22 04:03:11 2009] Checking for Bowtie index files
[Wed Jul 22 04:03:11 2009] Checking for reference FASTA file
[Wed Jul 22 04:03:11 2009] Checking for Bowtie
Traceback (most recent call last):
File "../tophat", line 1484, in <module>
sys.exit(main())
File "../tophat", line 1420, in main
check_bowtie()
File "../tophat", line 567, in check_bowtie
bowtie_version = get_bowtie_version()
File "../tophat", line 548, in get_bowtie_version
proc = subprocess.Popen(['bowtie', '--version'],stdout=subprocess.PIPE)
File "/usr/lib/python2.5/subprocess.py", line 594, in __init__
errread, errwrite)
File "/usr/lib/python2.5/subprocess.py", line 1147, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
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