parameter combination problem

[bernt-matthias]

When running:

cd-hit -i "/tmp/tmpN5gjOx/files/000/dataset_4.dat" -o rep_seq -c 0.9 -n 5 -t 2  -b 20 -l 10 -G 0 -aL 0.0  -AL 99999999  -aS 0.0  -AS 99999999 -A 0 -s 0.0 -S 999999 -uL 1.0 -uS 1.0 -U 99999999 -g 0 -B 0 -p 1 -d 40 -M 0

I get the following output:

================================================================
Program: CD-HIT, V4.6 (+OpenMP), Nov 09 2015, 20:39:49
Command: cd-hit -i /tmp/tmpN5gjOx/files/000/dataset_4.dat -o
         rep_seq -c 0.9 -n 5 -t 2 -b 20 -l 10 -G 0 -aL 0.0 -AL
         99999999 -aS 0.0 -AS 99999999 -A 0 -s 0.0 -S 999999
         -uL 1.0 -uS 1.0 -U 99999999 -g 0 -B 0 -p 1 -d 40 -M 0

Started: Fri Feb 23 18:40:11 2018
================================================================
                            Output                              
----------------------------------------------------------------

Fatal Error:
You are using local identity, but no -aS -aL -A option
Program halted !!

But the three options are set.

[bernt-matthias]

Ah, it seems that -aS and -aL need to be > 0 (the default). I guess changing the default would help.