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Old 07-23-2009, 09:25 AM   #1
pfranchini
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Location: Cape Town

Join Date: May 2009
Posts: 19
Default TopHat running error

Hi,
I found the same problem of boahua100 while running tophat. I moved the executable files bowtie, bowtie-inspect e bowtie-build in the same path where tophat, the reference file and the reads file are but:

student@410083:~/Desktop/tophat-1.0.9/PROVA$ ./tophat -o GINO -m 2 -G pizzolo.gff Scaffold_bowtizzato Reads1

[Thu Jul 23 18:09:15 2009] Beginning TopHat run (v1.0.9)
-----------------------------------------------
[Thu Jul 23 18:09:15 2009] Preparing output location GINO/
[Thu Jul 23 18:09:15 2009] Checking for Bowtie index files
[Thu Jul 23 18:09:15 2009] Checking for reference FASTA file
[Thu Jul 23 18:09:15 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/python2.6/subprocess.py", line 595, in __init__
errread, errwrite)
File "/usr/lib/python2.6/subprocess.py", line 1092, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
student@410083:~/Desktop/tophat-1.0.9/PROVA$

Any suggestions?

Thanks!!

P
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Old 08-05-2009, 08:39 PM   #2
chengeng
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Location: china

Join Date: Jul 2009
Posts: 14
Default

Quote:
Originally Posted by pfranchini View Post
Hi,
I found the same problem of boahua100 while running tophat. I moved the executable files bowtie, bowtie-inspect e bowtie-build in the same path where tophat, the reference file and the reads file are but:

student@410083:~/Desktop/tophat-1.0.9/PROVA$ ./tophat -o GINO -m 2 -G pizzolo.gff Scaffold_bowtizzato Reads1

[Thu Jul 23 18:09:15 2009] Beginning TopHat run (v1.0.9)
-----------------------------------------------
[Thu Jul 23 18:09:15 2009] Preparing output location GINO/
[Thu Jul 23 18:09:15 2009] Checking for Bowtie index files
[Thu Jul 23 18:09:15 2009] Checking for reference FASTA file
[Thu Jul 23 18:09:15 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/python2.6/subprocess.py", line 595, in __init__
errread, errwrite)
File "/usr/lib/python2.6/subprocess.py", line 1092, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
student@410083:~/Desktop/tophat-1.0.9/PROVA$

Any suggestions?

Thanks!!

P


Hi,
I was ever met such errors.This happens when you don't put bowtie in your PATH.

Geng
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Old 08-10-2009, 07:46 AM   #3
pfranchini
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Location: Cape Town

Join Date: May 2009
Posts: 19
Default

Thanks,
I checked again and bowtie was not in the PATH..Now I put it there and TopHat correctly works.

Paolo
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