Cd-Hit-Est-2D Segmentation Fault
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12.4 years ago

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.

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

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

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12.4 years ago
Chris ▴ 190

Try a

ulimit -s unlimited

before running cd-hit.

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I believe it's already unlimited.

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12.4 years ago
Burlappsack ▴ 690

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?

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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/

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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.

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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
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