[Bioperl-l] Error in tempfile() using /tmp/XXXXXXXXXX: Could not create temp /usr/local/lib/perl5/site_perl/5.8.0/Bio/Root/IO.pm line 473

Samuel Andersson samuel at thep.lu.se
Mon Feb 24 15:59:18 EST 2003


Hi!
I am not able to solve this problem, even though i used completly new
version of Bioperl...
Can you please help me.....
I am getting  Error  when i am trying to blast more than 526 sequences....
Here
is the sample code...

#!/usr/local/bin/perl -w

BEGIN {
    $ENV{'BLASTDIR'}="/usr/local/packages/blast";
}

use Bio::Seq;
use Bio::Tools::BPbl2seq;
use Bio::Tools::Run::StandAloneBlast;

my $input1=Bio::Seq->new( -seq =>
"AAAAAAAAAAAAtcttcgcgcgcgtctcggctcgctctgcgcgcgcgcgcttcgagacgagctcagacgactagcgactacgagcatcgacgatcagcagctacgacgagcgactacgacgagcactacgagcagcatctgacgagcatctacgacgactacgacgactacgacgacgacgacttacgacgactactacggacaAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",-id
=> 'ref_seq');
my $input2=Bio::Seq->new( -seq =>
"AAAAAAAAAAacactactacgagcatacAAAAAAAAAAAAAAAAAAAAAA"   ,-id  => 'q_seq');

for (my $i=1; $i<526; $i++) {
    my $factory = Bio::Tools::Run::StandAloneBlast->new('program' =>
'blastn', 'outfile' => 'bl2seq.out');
    my $BPbl2seqobj = $factory->bl2seq($input2, $input1);
    eval{
        $hsp = $BPbl2seqobj->next_feature();
    };
}


Error: Error in tempfile() using /tmp/XXXXXXXXXX: Could not create temp
file /tmp/enaaesDUKO: Too many open files at
/usr/local/lib/perl5/site_perl/5.8.0/Bio/Root/IO.pm line 473
Thank you

/Samuel




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