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-   -   CISA assembly contig integrator error (http://seqanswers.com/forums/showthread.php?t=33890)

gmarco 09-20-2013 12:31 AM

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

gmarco 09-23-2013 11:54 PM

Seem to be a directory permission issue. CISA doesn't like NFS mount directories..

yifangt 02-19-2014 08:15 AM

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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