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

[Steven Cannon]

Peter:

Thanks. Actually, eval didn't help, at least as I applied it -- the 
program keeps chugging (and ignores the errors), but the blasts still 
don't give output after the ~250th hit. So I still wonder if  the bl2seq 
problem might be the origin of the bioperl bl2seq errors.

Steve

On Thursday, April 17, 2003, at 10:12 AM, Peter Schattner wrote:

> 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
>
>