sarahet

I did some tests and RAM decreased to 170GB from previous 214 GB, but the runtime increased again from previous 40 minutes to now 1:10h. I think we probably need...

Thanks a lot for your reply. I did not set this option because according to the help message, I thought the ```--alignment-mode 3``` is set by default: ``` --alignment-mode INT...

I see, thanks. When I run the command with ```-a``` I get the following verbose output: ``` MMseqs Version: 6f45232ac8daca14e354ae320a4359056ec524c2 Substitution matrix aa:blosum62.out,nucl:nucleotide.out Add backtrace true Alignment mode 3 Alignment...

Hi - could this link be the problem by chance? https://github.com/seqan/lambda/blob/cf59351539c7d270171524fab20b8fff3e2bec06/src/mkindex_options.hpp#L120 At least it is longer than 80 char and can't just be split. If so, do you have a...

Hi Bryony, I am sorry that you encounter this problem. Do you have the chance to run it locally outside of your HPC with a small test example to see...

Hi - can you elaborate a bit why you would like to have this feature and how exactly you would like the calculation to work in comparison to the current...

I think that is doable. The reason why we excluded them mainly is that especially for scores like entropy, it harms the computation (we cannot compute entropy if out of...