[Bioperl-l] SeqIO problem on fasta file with large number of sequences.

Kun Zhang kzhang@gsbs3.gs.uth.tmc.edu
Mon, 08 Oct 2001 15:12:36 -0500

Hello! I'm using SeqIO to read DNA sequences of NCBI's unigene cluster, 
which is distributed as a big fasta file 
(ftp://ftp.ncbi.nlm.nih.gov/pub/schuler/unigene/Hs.seq.uniq.Z), and process 
every gene sequentially. I got the following error message when 1002 (or 
1003) sequences have been processed.
Error in tempfile() using /tmp/XXXXXXXXXX: Could not create temp file 
/tmp/eo0UwZVasW: Too many open files at 
/usr/lib/perl5/site_perl/5.6.0/Bio/Root/IO.pm line 41

However, I check the /tmp directory, and found not a single temporary 
sequence. Is there any way to work around this problem except for chopping 
the fasta file into several smaller ones? Thanks!

Kun Zhang
Human Genetics Center
UT-Houston Health Science Center