Milot Mirdita

The cns column stores the consensus sequences. That is not an actual sequence contained in the DB, but computed from the profile.

You can pass report-mode directly to easy-taxonomy then you get Krona output directly. Otherwise you have to use the non-easy modules to call taxonomyreport directly. I can provide more detailed...

``` mmseqs easy-taxonomy query.fasta database result tmp --report-mode 1 ``` The result_report file is a HTML file that can be open with a webbrowser. I did not try with Kalamari,...

To slightly expand on this, `easy-cluster` just calls `cluster` and a few modules to make the clustering tsv file and the FASTA files. It itself doesn't do anything special, however...

Search worked correctly, but the taxonomy step did not work? Did the search step happen to fill the file system completely?

`result` is placed in the same working directory where you executed the command. The `/tmp/mydir` folder is not needed after a command was successfully executed, which seems to be the...

I have recently migrated the binary server to a different machine since the old one was full. The new server seems to have the issue that the first requests fails...

From what I can tell this is not actually an SSL issue. Something in our network completely eats the first packet, and nothing appears on the server. Subsequent requests appear...

You can achieve this by manually cascading your clustering steps. We have implemented something like this a long time ago for Uniclust (https://github.com/milot-mirdita/uniclust-pipeline/blob/9b37347d1e9bb0153efcb986b5d828f9f4a316f0/uniclust_workflow.sh#LL67C7-L128C24). However, this script is not up-to-date, but...

Sorry this one i meant: https://github.com/soedinglab/uniclust-pipeline/blob/ec52afc312baab5178ce709caebb41bbae9bb3f0/uniclust_workflow.sh#L49-L133