Lotus2 does not read -taxAligner

[Justin Stewart]

Hello Falk, 

I am trying out your lovely program on some ITS2 data. A problem keeps occuring where I can create VT using the Vsearch method but when I try to classify taxonomy it defaults to RDB. Likewise it thinks I am using bacterial sequences when I am not. 

If you have any input that would be greatyl appreciated.

Justin Stewart

Error code:

"RefDB UNITE requested, but -taxAligner set to "0": therefore RDP classification of reads will be done"

My commands: 

lotus2 -i Seqs \

-o lotus2 \

-m TestMap.txt \

-refDB UNITE \ 

-amplicon_type ITS2 \ 

-tax_group fungi \ 

-taxAligner blast \

 -clustering vsearch \

 -id 0.97

[Falk Hildebrand]

Hey Justin, this likely refers to a problem with arg parsing, that I suspected has been fixed in the latest versions now (avaialble on github). If you could run with these again, that might already solve the problem.

best,

Falk

[Justin Stewart]

Thanks! this helped!