Error running oases_pipeline python script

[InesSoriguer]

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!!

[2seq]

Did you determine what the problem was? I am having the same trouble.

[mastal]

Error running oases_pipeline python script

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?

[2seq]

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!

[seqguy]

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/