[Bioperl-l] Blast temporary open files not closed
ende
mmacho at gmail.com
Sat Sep 9 23:50:10 UTC 2006
Thank all of you for your quick and precise answer!!!
My bioperl version must be 1.20 :(
I can read it in the file Bio::Perl.pm since
perl -MCPAN -e shell
and then
i Bio::Perl
does not inform me about any local version but says instead:
trange distribution name [Bio:Perl]
Module id = Bio::Perl
CPAN_USERID BIRNEY (Ewan Birney <birney at sanger.ac.uk>)
CPAN_VERSION undef
CPAN_FILE B/BI/BIRNEY/bioperl-1.4.tar.gz
UPLOAD_DATE 2003-12-23
DSLIP_STATUS (,,,,)
MANPAGE Bio::Perl - Functional access to BioPerl for people
who don't know objects
INST_FILE /Library/Perl/5.8.6/Bio/Perl.pm
INST_VERSION undef
I read 1.20 at top of /Library/5.8.6/Bio/Perl.pm file!
After many (many) attempts of installing Bio::Perl via -MCPAN always
it ends with the same message (of course using force!!):
Failed 3/25 tests, 88.00% okay
t/WABA.......................ok
t/XEMBL_DB...................SOAP::Lite and/or XML::DOM not
installed. This means that Bio::DB::XEMBL module is not usable.
Skipping tests.
t/XEMBL_DB...................ok
Failed Test Stat Wstat Total Fail Failed List of Failed
------------------------------------------------------------------------
-------
t/BioFetch_DB.t 27 1 3.70% 8
t/EMBL_DB.t 15 3 20.00% 6 13-14
t/Ontology.t 255 65280 50 100 200.00% 1-50
t/TreeIO.t 41 1 2.44% 42
t/Variation_IO.t 25 3 12.00% 15 20 25
t/simpleGOparser.t 255 65280 98 196 200.00% 1-98
121 subtests skipped.
Failed 6/179 test scripts, 96.65% okay. 154/8273 subtests failed,
98.14% okay.
make: *** [test_dynamic] Error 2
/usr/bin/make test -- NOT OK
Running make install
make test had returned bad status, won't install without force
Failed during this command:
BIRNEY/bioperl-1.4.tar.gz : make_test NO
..and I am using "force" (exactly:)
cpan> force install B/BI/BIRNEY/bioperl-1.4.tar.gz
I have installed many other modules without no problems but this
seems to reject me. Finally I have dowloaded the bioperl
1.5.1 .tar.gz and installed ignoring the many errors make test gave
me. sudo make install and wow!!! the bioperl version changed and
lsof +p pidofperl | grep stat | wc -l
again grows during the execution until reach 250 (!) and crashes.
It was also imposible from CPAN shell to obtain the local bioperl
version (as was also impossible in a remote Linux installation, that
also said) INST_VERSION undef.
But now the Bio/Perl.pm file heads:
# Perl.pm,v 1.23.2.1 2005/10/09 15:16:18 jason Exp
#
# BioPerl module for Bio::Perl
(I am using 10.4.7 on the MacOSX)
the code launch blast all for each seq inside a perl object (use of
$blastMachine->io->_io_cleanup(); did not resolve the problem)
> sub DoBlastSeq ($$$$) {
> my ($self, $db, $seq, $outFileName) = @_;
> my %params = (
> program => "blastn",
> outfile => $outFileName,
> database => "$self->{path_db}/$db",
> # q => "-5",
> G => 3, # si
> E => 3, # si
> F => "\"m D\"", # "mD", # si
> e => 700, # si
> Y => 1.75e12, # si
> best => 1,
> );
> if (!$params{outfile}) {
> delete $params{outfile};
> }
> my $outErrs = ($outFileName || "blastErrs.err"),
>
>
> my $blastMachine = Bio::Tools::Run::StandAloneBlast->new(%params);
>
> open(OLDSTDERR, ">&", \*STDERR) or die "Can't dup STDERR: $!";
> open(STDERR, ">", $outErrs ) or die "ERROR reopening STDERR: $!";
>
> print "Running Blast with id: ", $seq->id(), "\n" if $DEBUG;
>
> my $blastResult = $blastMachine->blastall($seq);
>
>
> close(STDERR);
> open(STDERR, ">&", \*OLDSTDERR) or die "Can't dup OLDSTDERR: $!";
> unlink ($outErrs) if (-z $outErrs);
>
> return $blastResult;
> }
El 09/09/2006, a las 15:45, Brian Osborne escribió:
> Juan,
>
> I recall a bug like this was fixed a while back - what version
> Bioperl are
> you using? By the way, always give version numbers when reporting a
> bug, the
> answer "already fixed" is very common.
>
> Brian O.
>
>
> On 9/9/06 4:31 AM, "ende" <mmacho at gmail.com> wrote:
>
>>
>> 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
>> 19280 1589055 /usr/bin/perl
>> perl 21977 juanfc txt VREG 14,7 23476 1580272 /System/
>> Library/Perl/5.8.6/darwin-thread-multi-2level/auto/IO/IO.bundle
>> perl 21977 juanfc txt VREG 14,7 17772 1580263 /System/
>> Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Fcntl/Fcntl.bundle
>> perl 21977 juanfc txt VREG 14,7 114116 1580381 /System/
>> Library/Perl/5.8.6/darwin-thread-multi-2level/auto/POSIX/POSIX.bundle
>> perl 21977 juanfc txt VREG 14,7 23684 1580265 /System/
>> Library/Perl/5.8.6/darwin-thread-multi-2level/auto/File/Glob/
>> Glob.bundle
>> perl 21977 juanfc txt VREG 14,7 1797788 6275687 /usr/lib/
>> dyld
>> perl 21977 juanfc txt VREG 14,7 4379472 6276030 /usr/lib/
>> libSystem.B.dylib
>> perl 21977 juanfc txt VREG 14,7 1086420 6276221 /System/
>> Library/Perl/5.8.6/darwin-thread-multi-2level/CORE/libperl.dylib
>> perl 21977 juanfc 0u VCHR 4,2 0t3748 63113092 /dev/ttyp2
>> perl 21977 juanfc 1u VCHR 4,2 0t3748 63113092 /dev/ttyp2
>> perl 21977 juanfc 2u VCHR 4,2 0t3748 63113092 /dev/ttyp2
>> perl 21977 juanfc 3u VCHR 4,2 0t3748 63113092 /dev/ttyp2
>> perl 21977 juanfc 4r VREG stat(/
>> ...
>> Please, help.
>>
>>
>> --
>> Juan Falgueras
>> Profesor del Depto. de Lenguajes y Ciencias de la Computación
>> Universidad de Málaga
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
---- ende
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