Anton Savchenko
Anton Savchenko
Hi @pieterprovoost . I had a similar problem, and what helped was `--spaced-kmer-mode 0`
Thanks, it will be much appreciated! Either fasta headers or a separate table would be great to have. BTW, I see that temp files in my case grew up to...
Thanks for the fast answer! It is good to be aware of `inclusive` and `exclusive` methods, it explains some cases. Are they used in a mix, taxon by taxon, or...
Thanks. It is of course will not be suitable for concatenated tree, but will be surely useful for many other things.
Same with `mmseqs search --format-mode` : `Unrecognized parameter "--format-mode". Did you mean "--alignment-mode" (Alignment mode)?` UPD: I realized that these options are for `easy-search` probably, not for `search `
Now I see why `--exhaustive-search` works better - it swaps query and target. And you are right, high `--max-seqs` somewhere between 50 000 and 100 000 started to pick up...
I followed #901 and `--spaced-kmer-mode 0` did the trick for nucleotides; the rest of params were default (`-k 15 --max-seqs 300`).
First of all, thanks for the great viewer - using it for many years, still unmatched. This is additional details to the cropping bug. I first reported this in #1345,...
Thanks for the fast reply! Well, it's probably even worse - I tried on eukaryotes (fungi). It is just that we are constantly searching for better ways to assemble genomes...