The size of this alignment is forcing it to generate more build files than 
your system's open file limit.  The solution will have to be to close some 
of the files that we are not currently writing to (and reopen them in 
append mode if we need to write more data to them later).  Presumably it 
would track the order in which it has written to the files (from most 
recently to least recently) and close the one that it used least recently. 
 Basically, there's a build_ifile[] array in NLMSA.readMAFfiles(), and two 
lines where it writes to those by calling saveInterval().  I have a pretty 
clear idea of how to implement this, but can't work on this right away.  If 
you want I can describe how this could be implemented...

Yours,

Chris

On Thursday, April 25, 2013 12:42:34 PM UTC-7, Paul Rigor wrote:
>
> Hi Chris and community,
>
> So after applying the modifications according to pyrex, we're now 
> encountering the following IO error message on a machine with ulimit 
> (soft/hard) already set to 4096. 
>
> The error message follows:
> IOError: unable to open in write mode: 
> /extra/baldig1/genomics/pygrdata/alignments/MOUSE/mm10/multiz60way/3967.build
>
>

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