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soedinglab / MMseqs2-App

MMseqs2 app to run on your workstation or servers
https://search.foldseek.com
GNU General Public License v3.0
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App does not work with latest mmseqs version #61

Closed samirelanduk closed 1 year ago

samirelanduk commented 1 year ago

I am trying to replicate the commands that run in worker.go - specifically the MsaJob script that starts at: https://github.com/soedinglab/MMseqs2-App/blob/59f2761c2f215ed05e3c99879e97fa578f7c12cb/backend/worker.go#L273

When trying to run the expandaln line:

"${MMSEQS}" expandaln "${BASE}/qdb" "${DB1}.idx" "${BASE}/res" "${DB1}.idx" "${BASE}/res_exp" ${EXPAND_PARAM}

I get the error:

Unrecognized parameter "--expand-filter-clusters". Did you mean "--expansion-mode" (Expansion mode)?

This is using mmseqs 13-45111 (the latest version) - is the app supposed to be used with an older version of mmseqs which supported this parameter? Or with a modified/dev version of it?

I encountered a similar issue with some of the other scripts.

To clarify I have not spun up the entire app, I am just trying to get that generated bash script to run in isolation against the latest mmseqs command line tool. Is there something I'm missing?

samirelanduk commented 1 year ago

Looks like this app uses a much more recent commit of mmseqs, whereas there hasn't been an official release of mmseqs in some time so the version installable with (for example) Brew doesn't work with this app. I guess this can be resolved by just using the Dockerfile provided here to build the relevant mmseqs.

milot-mirdita commented 1 year ago

The latest MMseqs2 release 14 includes everything required to run the app.