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Old 09-20-2013, 12:31 AM   #1
gmarco
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Location: Spain

Join Date: Oct 2012
Posts: 36
Question CISA assembly contig integrator error

Hello,

I'm trying to use CISA to merge and optimize two de novo bacterial assemblies.
Process seems to work fine until the very last step. I'm getting this error:

Code:
Traceback (most recent call last):
  File "CISA.py", line 63, in <module>
    os.rename('Contigs_'+final+'.fa',outfile)
OSError: [Errno 18] Invalid cross-device link
I've chmoded all dirs to 755. And I'm the owner of all the dirs.

Any idea how to troubleshot this?

CISA website: http://sb.nhri.org.tw/CISA/en/CISA
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Old 09-23-2013, 11:54 PM   #2
gmarco
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Default

Seem to be a directory permission issue. CISA doesn't like NFS mount directories..
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Old 02-19-2014, 08:15 AM   #3
yifangt
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Location: Canada

Join Date: Feb 2011
Posts: 61
Default solution to OSError

I met same problem. Did a little bit search and found out one solution can be:
Code:
import shutil
then change this line (Line 64 at CISA.py )
Code:
   os.rename('Contigs_'+final+'.fa',outfile)
to
Code:
shutil.move('Contigs_'+final+'.fa',outfile)
It worked for me.
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