Problem with identity threshold

[sagnikbanerjee15]

Hello,

I am running cd-hit-est on a file and I am getting an error when I set the threshold to any value below 0.8. I am making required alterations in the value of n with regards to the identity threshold. This is the exact error I am getting:

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

Thank you.

[zhenhua-zhang]

I encountered the same problem and tried to modify its source. But I don't know the influence. @daokoder @weizhongli

[smsaladi]

bump ... since from the user's guide, this should work along with modifying the word size

for example, for cd-hit-est

-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 

[bobeobibo]

I'm having the same issue on cd-hit-est, even with recommended word sizes.

[jalwillcox]

I ran into this same problem. I don't know why it happens, but I switched to using psi-cd-hit.pl, e.g. something like

psi-cd-hit.pl -i input.fa -o output -c 0.75 -prog blastn

That seems to work - I hope it's helpful to others!