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    CD-HIT: Sequence clustering software - Support tickets

    Submit | Open tickets | Closed tickets

    [ 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.
    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
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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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