[Bioperl-l] Blast temporary open files not closed

Chris Fields cjfields at uiuc.edu
Sat Sep 9 14:06:47 EDT 2006


According to the mail list archives the tempfie issue with StandAloneBlast
was supposed to be fixed by version 1.4.  

http://article.gmane.org/gmane.comp.lang.perl.bio.general/4677

The above post also has a possible fix (using
'$factory->io->_io_cleanup()').

As has been previously mentioned by Brian and Hilmar, having example code,
the OS, and the bioperl version would help in future posts.

Chris

> 	Processing a fasta file with about 500 dna seqs.. my MacOSX (that
> has the max number of opened files up to 512) crashes... You need to
> divide the problem in pieces or (in bash shell, with ulimit -n 1024)
> augment that max number of opened files.
> 
> This has no sense for me since my perl program nor leave any open
> file without its corresponding closing. On the other side, the
> problem arises when the number of dnas grows _in one file_.
> 
> In the code I run blast (StandAloneBlast... $blastMachine->blastall)
> for each seq.
> 
> 
> Then sniffing int the perl program stopped perl program I confirmed
> my suspects.  BioPerl (StandAloneBlast) does not closes temporary
> opened files.  Those files seems to be created to save seqs for to be
> then processed by blastall program...  The output of lsof indicates
> (as MacOSX System Monitor) that those files are left opened but not
> there (!?)
> 
> The output of  lsof +p pidofperlprogram
> 
> COMMAND   PID   USER   FD   TYPE DEVICE SIZE/OFF     NODE NAME
> perl    21977 juanfc  cwd   VDIR   14,7      238  6835993 /Users/
> juanfc/Documents/programperl    21977 juanfc  txt   VREG   14,7
....
> perl    21977 juanfc  102r  VREG                          stat(/
> private/tmp/5wrMPduqip): No such file or directory
> perl    21977 juanfc  103r  VREG                          stat(/
> private/tmp/O5rhMCu28A): No such file or directory
> 
> 
> 
> Please, help.
> 
> 
> --
>      Juan Falgueras
>      Profesor del Depto. de Lenguajes y Ciencias de la Computación
>      Universidad de Málaga


Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign




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