[Bioperl-l] Blast temporary open files not closed
cjfields at uiuc.edu
Sat Sep 9 18:06:47 UTC 2006
According to the mail list archives the tempfie issue with StandAloneBlast
was supposed to be fixed by version 1.4.
The above post also has a possible fix (using
As has been previously mentioned by Brian and Hilmar, having example code,
the OS, and the bioperl version would help in future posts.
> 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
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign
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