Open GoogleCodeExporter opened 8 years ago
I also have these problem, it occurs when adding the attached file to my fasta
files for clustering. using cd-hit-est only with default parameters and -c 0.95
Original comment by Hoelzer....@gmail.com
on 5 Nov 2013 at 2:43
Attachments:
I've also experienced this problem with the attached file and the following
command. The issue is present with versions 4.6 and 4.6.1.
cd-hit-est -i single_transcript_hits.fasta -o testout.fasta -d 0 -c 1.0 -p 1
Original comment by kweitem...@gmail.com
on 15 Jul 2014 at 4:52
Attachments:
The problem is that CD-HIT's new (as of 4.6) way of computing the number of max
sequences in Options::ComputeTableLimits doesn't account for huge values of
max_entries (in cdhit-common.c++). However, the new way of calculating
max_entries seems to generate staggeringly large values. It then calculates the
ratio of max_sequences to max_entries, which ends up having an effective value
of 0 given the colossal denominator, but then it never checks to see if
max_sequences has a value of 0.
This causes an infinite loop later in the program (SequenceDB::DoClustering,
loop at line 2937): max_seqs is 0, so the first while loop is never executed,
meaning m is never incremented.
The attached patch fixes it. I don't know if it's the author's original
intention but it works.
Also, note to the author: you changed the code to pass min_len to that function
instead of NAAN, but then you don't do anything with it! Perhaps that's the
source of the problem?
Original comment by inve...@ebi.ac.uk
on 22 Jul 2014 at 11:27
Attachments:
Note that there is a minor patch where minor changes (to improve the use of
long sequences) by the author and it is available here:
https://code.google.com/p/cdhit/source/detail?r=784a6f1b5e1175722462afbb0906c77e
85dfa556
I added the above correction (post#3) to this new version of cdhit-common.c++.
Remember to "make" again in the cd-hit directory after adding these corrections.
Original comment by t.dugede...@gmail.com
on 8 Aug 2014 at 3:13
Hi. Still having the infinite loop comparing sequences from 0 to 0. any other
changes that could help? I looked at the diff files and recompiled based on
those changes.
Original comment by solar...@uci.edu
on 13 Feb 2015 at 11:24
Original issue reported on code.google.com by
kyosh...@nig.ac.jp
on 29 Aug 2013 at 4:47Attachments: