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Old 07-25-2012, 06:56 AM   #1
figo1019
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Default tophat running error

hi All

I have installed the tophat with bowtie and samtools in the path but I am getting the error when I try to run the example file.
[2012-07-25 17:31:11] Beginning TopHat run (v2.0.4)
-----------------------------------------------
[2012-07-25 17:31:11] Checking for Bowtie
Bowtie version: 2.0.0.6
[2012-07-25 17:31:11] Checking for Samtools
Samtools version: 0.1.18.0
[2012-07-25 17:31:11] Checking for Bowtie index files
[2012-07-25 17:31:11] Checking for reference FASTA file
[2012-07-25 17:31:11] Generating SAM header for test_ref
format: fastq
quality scale: phred33 (default)
[2012-07-25 17:31:11] Preparing reads
left reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
right reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
Traceback (most recent call last):
File "./tophat", line 3948, in <module>
sys.exit(main())
File "./tophat", line 3912, in main
user_supplied_deletions)
File "./tophat", line 3362, in spliced_alignment
if reads == None or not nonzeroFile(reads):
File "./tophat", line 1053, in nonzeroFile
samtools_view = subprocess.Popen(samtools_view_cmd, stdout=subprocess.PIPE)
File "/usr/lib64/python2.6/subprocess.py", line 639, in __init__
errread, errwrite)
File "/usr/lib64/python2.6/subprocess.py", line 1228, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

Can any one help me in correcting this.

Regards
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Old 07-26-2012, 09:43 AM   #2
westerman
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Well, did you check to see if the file exists? E.g., /usr/lib64/python2.6/subprocess.py. If not then you will have to get it installed.
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Old 05-03-2013, 06:27 AM   #3
rpauly
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Did you find a solution for this? I am getting the same error.
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Old 05-03-2013, 06:43 AM   #4
westerman
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Perhaps the response I gave figo1019 worked? How about for you, rpauly? What does an

'ls -l /usr/lib64/python2.6/subprocess.py'

give?
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Old 05-03-2013, 06:51 AM   #5
rpauly
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Running 'ls -l /usr/lib64/python2.6/subprocess.py' Gives me:

-rw-r--r--. 1 root root 57049 Aug 28 2012 /usr/lib64/python2.6/subprocess.py


My entire error message is:

left reads: min. length=100, max. length=100, 14252846 kept reads (14942 discarded)
right reads: min. length=100, max. length=100, 14185363 kept reads (82425 discarded)
Traceback (most recent call last):
File "/usr/local/partekgs/partek_flow/bin/bowtie_two-1.0/tophat", line 4035, in <module>
sys.exit(main())
File "/usr/local/partekgs/partek_flow/bin/bowtie_two-1.0/tophat", line 4002, in main
user_supplied_deletions)
File "/usr/local/partekgs/partek_flow/bin/bowtie_two-1.0/tophat", line 3470, in spliced_alignment
if reads == None or not nonzeroFile(reads):
File "/usr/local/partekgs/partek_flow/bin/bowtie_two-1.0/tophat", line 1119, in nonzeroFile
samtools_view = subprocess.Popen(samtools_view_cmd, stdout=subprocess.PIPE)
File "/usr/lib64/python2.6/subprocess.py", line 639, in __init__
errread, errwrite)
File "/usr/lib64/python2.6/subprocess.py", line 1228, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
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Old 05-03-2013, 07:02 AM   #6
GenoMax
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rpauly: You are running this using partek flow software so this error may be best addressed by contacting Partek tech support. have you tried to contact them?
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Old 05-03-2013, 07:03 AM   #7
rpauly
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No, I just put the files in the flow directory but I am running it using the command line tophat option.
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Old 05-03-2013, 07:07 AM   #8
GenoMax
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Quote:
Originally Posted by rpauly View Post
No, I just put the files in the flow directory but I am running it using the command line tophat option.
Are you using tophat that is part of partek flow install?
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Old 05-03-2013, 07:16 AM   #9
westerman
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Now that I look at the Python code (subprocess.py) it is simply complaining about a missing data file. What file it, all too naturally, does not say. :-(
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Old 05-03-2013, 07:18 AM   #10
rpauly
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Never mind...fixed it!
samtools was not in the path...

Thanks everyone!

Rini
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