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[ Ticket #452 ] CD-HIT HANGING
Date:
05/06/08 10:37
Submitted by:
unset
Assigned to:
unset
Category:
Clustering
Priority:
5
Ticket group:
Critical
Resolution:
Unset
Summary:
CD-HIT HANGING
Original submission:
I am running CD-HIT against the current nr database (3.3G). It is running from past 4-5 days but not showing any progress (not printing any information) and has not given any memory error so far.

Is there any other way I can run CD-HIT against the nr database.
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Followups
Comment Date By
Thank you for your response. I will try it out. 08/26/08 08:05 taruna
I had same problem and contacted Weizhong Li. He hinted to me that the long description is the problem. I wrote the following small perl script using bioperl to remove the description of the fasta sequences.

CD-HIT works now.

#!/usr/local/bin/perl

use Bio::Seq;
use Bio::SeqIO;

$seqin = Bio::SeqIO->new( -format => 'Fasta', -file => 'nr.fasta');
$seqout= Bio::SeqIO->new( -format => 'Fasta', -file => '>nr_no_desc.fasta');

my $seq_count=0;

while (my $NextSeq = $seqin->next_seq())
{
$NextSeq->desc("");
$seqout->write_seq($NextSeq);
$seq_count = $seq_count+1;
}
print "Finished shortening descriptions of $seq_count sequences!n";
08/12/08 09:23 unset
I have the same problem as the gentleman above. 08/07/08 15:39 unset
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Ticket change history
Field Old value Date By
status_id Pending 07/14/11 01:22 liwz
close_date 12/31/69 19:00 07/14/11 01:22 liwz

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