How can run cd-hit-est with a clstr threshold less than 0.8?

Question

[m.koohi.m]

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

Answer 1

[NPalopoli]

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).

Answer 2

[Asaf]

For future reference

The 0.8 identity threshold for EST (nucleotides) is hardcoded. However, there's an option to use -D (distance) instead of -c (identity threshold). For some reason I couldn't find it in the documentation and couldn't figure out how it's being calculated.