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YoshitakaMo / localcolabfold

ColabFold on your local PC
MIT License
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Question: use of MMseqs2 locally, problem with the databases. #218

Closed crisdarbellay closed 6 months ago

crisdarbellay commented 8 months ago

Hello,

I tried to install and use localcolabfold entirely locally, on a HPC cluster. To do so, I followed the steps indicated for localcolabfold. I followed the instructions here: #203 for mmseqs2. However, I enconter a problem with the database COLABDB. When I follow the steps indicated here https://qiita.com/Ag_smith/items/bfcf94e701f1e6a2aa90 and run setup_database.sh, I have this error: /work/lpbs/colab_database/colabfold_envdb_202108_db.sh: line 21: 2565750 Killed "$MMSEQS" tsv2db "${IN}_h.tsv" "${OUT}_h" --output-dbtype 12 ${VERBOSITY} createindex colabfold_envdb_202108_db tmp2 --remove-tmp-files 1 ... Input colabfold_envdb_202108_db does not exist

How can I resolve this problem?

Thank you for your attention!

YoshitakaMo commented 8 months ago

Probably you failed the database setup at mmseqs tsv2exprofiledb "colabfold_envdb_202108" "colabfold_envdb_202108_db" line. This step is very time-consuming.

If you've already downloaded colabfold_envdb_202108.tar.gz in the directory, type mmseqs tsv2exprofiledb "colabfold_envdb_202108" "colabfold_envdb_202108_db" to resume the process. If it finishes successfully, then type mmseqs createindex "colabfold_envdb_202108_db" tmp2 --remove-tmp-files 1 and touch COLABDB_READY.