Date:
05/06/08 10:37
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Submitted by:
unset
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Assigned to:
unset
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Category:
Clustering
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Priority:
5
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Ticket group:
Critical
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Resolution:
Unset
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Summary:
CD-HIT HANGING
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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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Date
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By
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Thank you for your response. I will try it out.
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08/26/08 08:05
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taruna
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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";
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08/12/08 09:23
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unset
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I have the same problem as the gentleman above.
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08/07/08 15:39
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unset
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Ticket change history
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Field
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Old value
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Date
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By
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status_id
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Pending |
07/14/11 01:22
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liwz
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close_date
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12/31/69 19:00 |
07/14/11 01:22
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liwz
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