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Old 03-05-2014, 04:33 AM   #1
Junior Member
Location: Barcelona

Join Date: Oct 2013
Posts: 2
Post CD-HIT-EST-2D Error: segmentation fault ('core' dumped)


I am using CD-HIT-EST-2D in order to compare two contigs files in fasta format. I have been using it for several files and it worked properly until I got an error with two files. The error is: segmentation fault ('core' dumped). I give you the commands and the output:

[joel@localhost results]$ /programs/cd-hit-v4.6.1-2012-08-27/./cd-hit-est-2d -i Contig_Leg_500Mb.fasta -i2 Contig_Leg_500Mb_15ntout.fasta -o Prueb.fasta -c 0.95 -n 8
Program: CD-HIT, V4.6 (+OpenMP), Feb 26 2014, 12:02:11
Command: /programs/cd-hit-v4.6.1-2012-08-27/./cd-hit-est-2d -i
Contig_Leg_500Mb.fasta -i2
Contig_Leg_500Mb_15ntout.fasta -o Prueb.fasta -c 0.95
-n 8

Started: Mon Mar 3 12:03:48 2014
total seq in db1: 37276
total seq in db2: 28500
longest and shortest : 14632 and 201
Total letters: 19048606
Sequences have been sorted
longest and shortest : 12192 and 201
Total letters: 13606287

Approximated minimal memory consumption:
Sequence : 36M
Buffer : 1 X 15M = 15M
Table : 1 X 1M = 1M
Miscellaneous : 0M
Total : 54M

Table limit with the given memory limit:
Max number of representatives: 0
Max number of word counting entries: 93208177

Segmentation fault (`core' dumped)


I have checked the fasta files and they look good. Besides, I have tried to use CD-HIT-EST with each file and it worked, so I don't know where is the problem. I also used CD-HIT-EST-2D for files with more and larger sequences and it worked so the problem is not with the memory limitations.
Did someone have the same problem?

Joel_91 is offline   Reply With Quote
Old 05-21-2020, 01:11 PM   #2
Junior Member
Location: Brazil

Join Date: Aug 2019
Posts: 3

Hi Joel 91.
I have got the same problem. Have you fixed the issue?
Best regards.
fabio.marcelo is offline   Reply With Quote

cd-hit, clustering, core dumped

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