[Bioperl-l] looks like a Bio::SeqIO error

fungazid fungazid at yahoo.com
Fri May 15 09:17:34 EDT 2009


I hope this is the right address for bioperl programming issues. Bioperl
saves me a lot of time (not to re-invent the wheel), but there are some
extremely irritating problems (I would change the code myself if I knew

I am trying to read a file (~20MB) containing multiple fasta sequences:

with the following lines:

my $seqin = Bio::SeqIO->new('-format'=>'largefasta','-file'=>$file1);

LOOP1: while ( my $seqobj1 = $seqin->next_seq())

my $seq=$seqobj1->subseq(1,$seqobj1->length);

This works right for the first ~30000 contig sequences but then the
following message appears:

Error in tempdir() using /tmp/XXXXXXXXXX: Could not create directory
/tmp/6eS92VzVjm: Too many links at /usr/share/perl5/Bio/Root/IO.pm line 744

What to do ??? (this is only one of some different Bioperl related bugs that
I'm experiencing)

View this message in context: http://www.nabble.com/looks-like-a-Bio%3A%3ASeqIO-error-tp23559474p23559474.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.

More information about the Bioperl-l mailing list