Question: Segmentation fault for cd-hit
gravatar for Crystal
4.8 years ago by
United States
Crystal30 wrote:

Hello All,

I tried to compare two database and remove redundant sequences in one database by using cd-hits.

I do found someone in this forum had the same problem, but I didn't see the resolution on it.

The command I used is 

tools/cd-hit-v4.6.1-2012-08-27/cd-hit-est-2d -i V3_VFs.fas -i2 R1.ffn -G 0 -c 1.0 -AS 0 -AL 0 -aL 1.0 -aS 1.0 -o res2_R1_cdhitG

The output is like:




total seq in db1: 5927

total seq in db2: 2457

longest and shortest : 31497 and 78

Total letters: 7764226

Sequences have been sorted

longest and shortest : 16680 and 99

Total letters: 2818134

Approximated minimal memory consumption:

Sequence        : 10M

Buffer          : 1 X 15M = 15M

Table           : 1 X 16M = 16M

Miscellaneous   : 4M

Total           : 47M

Table limit with the given memory limit:

Max number of representatives: 0

Max number of word counting entries: 94035159

Segmentation fault

My colleague used the same code on her Mac to compare another two databases, and the code worked.

So how I solve my problem?




software error • 1.4k views
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