cd-hit threshold less than 0.7 is it possible??

Question

[casley_queiroz]

Hi,

Is it impossible to use 0.5 threshold identity in cd hit? I tried, I only managed using 0.7.

I used this command line:

$ cdhit -i secretome_cdhit.fasta -o clusters_50 -c 0.5 -n 5 -T 8

It shows this message:

Fatal Error:

Too low cluster threshold for the word length.

Increase the threshold or the tolerance, or decrease the word length.

Program halted !!

I know it's possible on the web server, but it takes a lot, due queue.

[casley_queiroz]

I got it!

Simple! Just use -n 3

$ cdhit -i secretome_cdhit.fasta -o clusters_50 -c 0.5 -n 3 -T 8