CD-HIT-EST not allowing below 80% cutoff

[roelofco]

I have been running the program applying various nt-identity cutoff values and the cd-hit-est does not allow for below 80%. Here is an exact example:

cd-hit-est -i /home/path/VP3.fasta -o /home/path/VP3.fasta -c .77000000000000000000 -n 4 -M 16000 -T 4

As you can see I have been applying -n flag as specified in the documentation, but still get the error.

[sapuizait]

So apparently there is no fix for this one?

[dralbishop]

I just encountered the same problem as noted above. I know that I need a lower than 80% identity threshold for my clustering, but when I run: cd-hit-est -i input.fasta -o output_75percent_word4 -c 0.75 -n 4 -M 1000 -T 8 -p 1

cd-hit-est gives an error and says: "Fatal Error: invalid clstr threshold, should >=0.8 Program halted !!"

Yet in the pdf manuals online it clearly says in the note about word size that 0.75 at least is acceptable: "Choose of word size: -n 8,9,10 for thresholds 0.90 ~ 1.0 -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"