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GTDB db not running with mmseqs2 taxonomy #967

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luigallucci opened this issue Mar 4, 2025 · 0 comments

luigallucci commented Mar 4, 2025 •

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Hi, thank you for the big work behind MMseqs2.

I tried to setup GTDB db (r220) as written in the WiKi.
In the folder I successfully get all the files indicated by the workflow:

taxonomy/
├── ar53_taxonomy_r220_reps.tsv
├── bac120_taxonomy_r220_reps.tsv
├── delnodes.dmp
├── gtdb_taxonomy.tsv
├── mapping
├── merged.dmp
├── names.dmp
├── nodes.dmp
├── ssu
├── ssu_all_r220.fna
├── ssu.dbtype
├── ssu_h
├── ssu_h.dbtype
├── ssu_h.index
├── ssu.index
├── ssu.lookup
├── ssu_mapping
├── ssu.source
├── ssu_taxonomy
└── tmp
    └── createindex.sh

The problems start when running mmseqs taxonomy on a contigs.fa.

Here, I get as error that is not able to find _nodes.dmp, _delnodes.dmp, _name.dmp etc.

Input taxonomy database "/bioinf/home/lgallucc/databases/gtdbtk/release220/taxonomy/" is missing files:
- /bioinf/home/lgallucc/databases/gtdbtk/release220/taxonomy/_mapping
- /bioinf/home/lgallucc/databases/gtdbtk/release220/taxonomy/_nodes.dmp
- /bioinf/home/lgallucc/databases/gtdbtk/release220/taxonomy/_names.dmp
- /bioinf/home/lgallucc/databases/gtdbtk/release220/taxonomy/_merged.dmp

I'm using the latest version of MMseqs2 on a conda env.

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