Hi.. I was trying the following script for extracting sequences in fasta format from a list of geneID from genbank. I got that error message when i tried large number of sequence download(some 1000-2000) at a time. the script does not work for large number of sequence to be extracted at a time. 

use Bio::Perl;
$database="genbank";
$format="fasta";
$pipe ="\\|";
$space = "    ";
open(INPUTFILE, "<test.txt");
while(<INPUTFILE>)
 {
   my($line) = $_;
   chomp($line);
   $line=~ s/$space/:/;
   $line=~ s/$pipe/$space/;
   $line=~ s/g/G/;
   $line=~ s/i/I/;
   $id= "$line";
#print "$id";
#print "\n";
   $sequence = get_sequence($database, $id);
   $test = write_sequence( ">>sequences_1.txt", $format, $sequence);
open (CHK , ">>checking.txt");
print CHK <<HERE;
$test
HERE
close CHK;
 }
 exit;

[download]

Thanks

In reply to problem when more then 2000 file downloading from database by sarf13

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