Question: How can run cd-hit-est with a clstr threshold less than 0.8?
0
gravatar for m.koohi.m
18 months ago by
m.koohi.m110
United States
m.koohi.m110 wrote:

Dear friends,

I try to run cd-hit-est with a cluster threshold less than 0.8 but every time I get the following error:

Fatal Error: invalid clstr threshold, should >=0.8 Program halted !!

I tried:

cd-hit-est -i seq.fasta -o out.fasta  -d 0 -T 10 -g 1 -M 10000 -c 0.6 -n 4

This command does not have any problem with cd-hit. The following command works well:

cd-hit -i seq.fasta -o out.fasta  -d 0 -T 10 -g 1 -M 10000 -c 0.6 -n 4

Am I missing something?

Thank you

cd-hit tools cluster • 907 views
ADD COMMENTlink modified 7 months ago by NPalopoli280 • written 18 months ago by m.koohi.m110
1
gravatar for NPalopoli
7 months ago by
NPalopoli280
Argentina/Buenos Aires/Universidad Nacional de Quilmes & Fundación Instituto Leloir
NPalopoli280 wrote:

According to the cd-hit-est manual you should use one of the following combinations of threshold (-c) and word size (-n):

-n 10, 11 for thresholds 0.95 ~ 1.0
-n 8,9 for thresholds 0.90 ~ 0.95
-n 7 for thresholds 0.88 ~ 0.9
-n 6 for thresholds 0.85 ~ 0.88
-n 5 for thresholds 0.80 ~ 0.85
-n 4 for thresholds 0.75 ~ 0.8

It escapes to me if lower thresholds are allowed and I don't have the correct input data at hand to try for myself (BTW, you should provide a sample dataset that would allow others to replicate the error).

ADD COMMENTlink written 7 months ago by NPalopoli280
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 539 users visited in the last hour