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Old 09-27-2012, 10:32 AM   #1
InesSoriguer
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Location: Sevilla

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Angry Error running oases_pipeline python script

Hello!

I'm very new in the world of bioinformatics, and maybe my question is so simple.

I'm trying to run the python script for the oases_pipeline, but it always give the same error.

The command I use is:

$python oases_pipeline.py -m 21 -M 31 -o outputfolder -d "-fastq -short /Users/geldoc/Desktop/TranscriptomePrograms/velvet_1.2.07/SecondRun/OW_sequence.txt" -p " -cov_cutoff 5 -min_trans_lgth 100 "

And the error is:

Could not find Velvet
Make sure that it is properly installed on your path

After this, I tried to run velvet without the python script and it works..so I don't understand the error message.... (I checked that the version of oases and velvet are right)

Thank you very much for your help!!
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Old 04-10-2013, 01:14 AM   #2
2seq
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Did you determine what the problem was? I am having the same trouble.
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Old 04-10-2013, 03:35 AM   #3
mastal
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Default Error running oases_pipeline python script

Quote:
Originally Posted by InesSoriguer View Post


After this, I tried to run velvet without the python script and it works..so I don't understand the error message.... (I checked that the version of oases and velvet are right)

What happens if you try

$velveth

from the same directory where you were running the python script?
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Old 04-10-2013, 03:37 AM   #4
2seq
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I think the problem is being caused by not enough memory. I am rerunning it with the output directory in a virtual directory with greater capacity. Hopefully this does the trick!
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Old 05-21-2013, 02:10 AM   #5
seqguy
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I think you need to change the location of velvet and oases in "subprocess.Popen" section of the oases_pipeline.py script or put the excecutables in /usr/local/bin/ or /usr/bin/
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