[Bioperl-l] SeqIO problem on fasta file with large number of sequences.
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!
Human Genetics Center
UT-Houston Health Science Center