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 > > -- You received this message because you are subscribed to the Google Groups "pygr-dev" group. To unsubscribe from this group and stop receiving emails from it, send an email to pygr-dev+unsubscr...@googlegroups.com. To post to this group, send email to pygr-dev@googlegroups.com. Visit this group at http://groups.google.com/group/pygr-dev?hl=en. For more options, visit https://groups.google.com/groups/opt_out.