Unrecognized parameter "--dbtype" when running easy-cluster

[laelbarlow]

Expected Behavior

Cluster structures in a given database made using foldseek createdb.

Current Behavior

When running easy-cluster on a very small set of 10 PDB structures, running the following command

foldseek easy-cluster ./target_db ./output_cluster ./tmp

results in this error message:

usage: foldseek createdb <i:PDB|mmCIF[.gz]> ... <i:PDB|mmCIF[.gz]> <o:sequenceDB> [options]
 By Martin Steinegger <[email protected]>
options: common:
 --threads INT   Number of CPU-cores used (all by default) [4]
 -v INT          Verbosity level: 0: quiet, 1: +errors, 2: +warnings, 3: +info [3]

examples:
 Convert PDB/mmCIF files to an db.

references:
 - Steinegger M, Soding J: MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology, 35(11), 1026-1028 (2017)
Unrecognized parameter "--dbtype". Did you mean "--threads" (Threads)?

Looks like perhaps foldseek easy-cluster is trying to run foldseek createdb with an outdated option.

Environment

I used the precompiled binary for osx from https://mmseqs.com/foldseek/

foldseek-osx-universal.tar.gz 09-Jul-2021 07:55 6998109

foldseek Version: 75bb2e3a2718903f47008d7d8cc3be099e35d1e9

Operating system version: macOS Catalina 10.15.7

[martin-steinegger]

Clustering is currently not implemented. Only the following commands should work

easy-search, createdb, align, aln2tmscore.

Foldseek is still under development.

[martin-steinegger]

Should be working now.