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[ Ticket #453 ] failing when long gene description
Date:
05/06/08 10:48
Submitted by:
unset 		Assigned to:
unset
Category:
Clustering 		Priority:
5
Ticket group:
Critical 		Resolution:
Unset
Summary:
failing when long gene description
Original submission:
I used cd-hit weekly to cluster nr.fa. Lately the program failed, just hanging, no reporting any progress nor any error. Thinking that nr.fa was too big I split it and submit by parts...all parts but 1 was clustered. Subdivided the failing part, re submiting, again all the parts but one was clustered...repeated the process several times, till got to the offendiing sequence

The annotation only is over 300K....still is a problem.
Do you think you can solve this?
Thanks

Raquel Norel
rn98@columbia.edu
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Followups
Comment Date By
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 09:24 unset
1 - Change in cd-hi.h the default value (300000):

For example with a new size of 600000:
#define MAX_DES 600000
#define MAX_LINE_SIZE 600000

2- Rebuild cd-hit application

05/30/08 14:56 chcaron
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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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