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.
|
Please log in to add comments and receive followups via email.
|
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
|
|
No results for "Dependent on ticket" |
No results for "Dependent on Task" |
No other tickets are dependent on this ticket
|
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
|
|