Non-existing flags in some tools

[bordin89]

Hi!

While trying to run the pipeline I found certain flags I had either to change manually in the code or not recognized altogether.

One issue is related to a reference to target-cov and --cov-mode. Are they interchangeable?

Unrecognized parameter --target-cov Did you mean "--cov-mode"?

Unrecognized parameter --max-seqs Did you mean "--max-seq-len"?

It seems that mmseqs got updated but probably the pipeline references a previous version of it?

Hope this helps!

[rubenbucio]

Did you find any way to make it work?? I'm stuck with "--target-cov"

[glucksfall]

I think "--target-cov" was changed to "-c" List matches above this fraction of aligned (covered) residues (see --cov-mode) [0.000]

[glucksfall]

I think "--max-seqs" doesn't exist anymore. I tracked changes in the code (src/commons/Parameters.cpp) and the option disappeared. I removed it from the script.