[Bioperl-l] tempfile problem with standalone blast

[Chris Fields]

You should post code examples that cause the problem (the more concise the better).  My guess is you are somehow caching the files by persisting the SearchIO instances; files for these are normally cleaned up when the SearchIO instance is destroyed.

If needed you can also call cleanup() from the standaloneblast instance to clean them up manually.

chris


On Jun 4, 2010, at 6:23 AM, Gopal wrote:

> Hi,
> 
> I am trying to run standalone blast and parse the files, both using BioPerl.
> 
> When running a moderately big file, I keep getting this message:
> 
> "Error in tempfile() using
> /var/folders/lJ/lJxoSpu4FYukooFDUoeLWIJTR5g/-Tmp-/XXXXXXXXXX: Could not
> create temp file
> /var/folders/lJ/lJxoSpu4FYukooFDUoeLWIJTR5g/-Tmp-/RLI8KU9LSL: Too many open
> files at /Library/Perl/5.10.0/Bio/Root/IO.pm line 719"
> 
> I am running on Mac OS Snow Leapord and my Perl, BioPerl are current.
> 
> please help me how to fix this problem,
> 
> thanks,
> 
> -gopal
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