Question: Cd-Hit-Est-2D Segmentation Fault
0
gravatar for Mariam Rizkallah
7.5 years ago by
Egypt
Mariam Rizkallah20 wrote:

Dear community,

I have a question regarding one of cd-hit suite utilities (cd-hit-est-2d) (http://weizhong-lab.ucsd.edu/cd-hit/). I downloaded it, compiled it and tried to use it, but each time I run it I got a segmentation fault.

./cd-hit-est-2d -i db1.fna -i2 db2.fna -o out -G 1 -n 10 -B 1 -p 1 -g 1 -c 0.98 -M 0 -T 0 > cd-hit-est.log &

I searched for it, I got a solution (http://www.bioinformatics.org/bugs/index.php?func=detailbug&bugid=1103&groupid=350) of changing stack_size but I can't find cd-hi-classic.c++ and my ulimit is already unlimited.

How to increase my stack_size?

Thank you.

• 3.5k views
ADD COMMENTlink modified 7.5 years ago by Chris190 • written 7.5 years ago by Mariam Rizkallah20

A 'segmentation fault' can mean multiple things, not just stack_size issues. How big are db1.fna & db2.fna ?

ADD REPLYlink written 7.5 years ago by Torst900

db1's size is 606 MB, while db2 is 6 MB.

ADD REPLYlink written 7.5 years ago by Mariam Rizkallah20
1
gravatar for Chris
7.5 years ago by
Chris190
Munich
Chris190 wrote:

Try a

ulimit -s unlimited

before running cd-hit.

ADD COMMENTlink written 7.5 years ago by Chris190

I believe it's already unlimited.

ADD REPLYlink written 7.5 years ago by Mariam Rizkallah20
0
gravatar for Burlappsack
7.5 years ago by
Burlappsack660
Burlappsack660 wrote:

Hello, If you've already increased the stack size and you are still getting a seg fault, you really need to find cd-hi-classic-c++ and make the suggested change. If you are having trouble locating the file(I had this problem today) might I suggest the find command?

ADD COMMENTlink written 7.5 years ago by Burlappsack660

I found it in an old version of cd-hit! cdhit-v4.2-2010-09-16/cd-hi-class.c++ However, I can't find it in the latest release cd-hit-v4.5.6-2011-09-02/

ADD REPLYlink written 7.5 years ago by Mariam Rizkallah20

yes, good idea. I have had to download previous versions of software to work around bugs. As long as the features are the same you should be fine.

ADD REPLYlink written 7.5 years ago by Burlappsack660

Did you solve the problem? I used the latest version (v4.6.1-2012-08-27), still encountered the same error when using cd-hit-est-2d. cd-hit-est works perfect, so I assumed that is not RAM problem. 

Also I tried to v4.2 you said, I had problem even when installing it. It reports the problem  'make: *** [cdhit-common.o] Error 1'

ADD REPLYlink written 4.1 years ago by sckinta510
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