[Bioperl-l] Re: "Too many files open" with bl2seq

[Peter Schattner]

Steven Cannon wrote:

> To second your '"Too many files open" with bl2seq' question, I noticed
> something similar last month when trying to use bl2seq via bioperl. So,
> apologies for re-posting, but maybe the extra details will help someone
> spot the glitch. I see a different set of errors (MSG:  No hit object
> found for bl2seq report  ... etc.) , but perhaps the underlying cause is
> the same.
>

Steve

Actually, these are two completely separate issues.  The "MSG:  No hit object
found for bl2seq report" crash is a bug in BPbl2seq.pm (I think).  Could you
submit this as a bug report?  I've seen this problem too and as a workaround
you can just surround the StandAloneBlast call to bl2seq in an "eval", ignore
the error and (at least for me) everything works fine.

The "Too many files open"  crash is something quite different.  It has
nothing to do with Bioperl since it happens when running bl2seq from the
command line as well.

Peter