Entering edit mode
7.4 years ago
casley_queiroz
▴
20
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.
I got it!
Simple! Just use -n 3
$ cdhit -i secretome_cdhit.fasta -o clusters_50 -c 0.5 -n 3 -T 8