CISA assembly contig integrator error

[gmarco]

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:

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]

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

[yifangt]

solution to OSError

I met same problem. Did a little bit search and found out one solution can be:

import shutil

then change this line (Line 64 at CISA.py )

   os.rename('Contigs_'+final+'.fa',outfile)

to

shutil.move('Contigs_'+final+'.fa',outfile)

It worked for me.