Problem with using custom phold database

[rozwalak]

• phold version: 0.1.4
• Python version: 3.11
• Operating System: Linux

Description

Hi,
I'm trying to make my own database using phold createdb and run some protein sequences against this newly create db.

What I Did

I started with "phold proteins-predict" for my custom protein set. Next, I ran "phold createdb" using the output from the previous step. Finally, I tried to compare my protein sequences (after proteins-predict) with the newly created custom database.

However, I encountered a warning:
"Phold Database file my_foldseek_db/phold_foldseek_db/all_phold_prostt5 is missing."

And an error:
"Phold database not found. Please run phold install -d my_foldseek_db/ to download and install the phold database."

So, I ran "phold install -d my_foldseek_db/" but it resulted in the installation of the full phold database instead of creating a usable custom database as I expected.

Moreover, is it possible to create my own database based only on Prost5, without PDB structures?

Below is the log from "phold createdb." It seems that the database was created correctly.

2024-06-26 06:34:10.652 | INFO     | phold.utils.util:begin_phold:72 - phold: annotating phage genomes with protein structures
2024-06-26 06:34:10.653 | INFO     | phold.utils.util:begin_phold:74 - You are using phold version 0.1.4
2024-06-26 06:34:10.653 | INFO     | phold.utils.util:begin_phold:75 - Repository homepage is https://github.com/gbouras13/phold
2024-06-26 06:34:10.654 | INFO     | phold.utils.util:begin_phold:76 - You are running phold createdb
2024-06-26 06:34:10.654 | INFO     | phold.utils.util:begin_phold:77 - Listing parameters
2024-06-26 06:34:10.654 | INFO     | phold.utils.util:begin_phold:79 - Parameter: --fasta_aa phold_08_phrogs_train/phold_aa.fasta
2024-06-26 06:34:10.654 | INFO     | phold.utils.util:begin_phold:79 - Parameter: --fasta_3di phold_08_phrogs_train/phold_3di.fasta
2024-06-26 06:34:10.654 | INFO     | phold.utils.util:begin_phold:79 - Parameter: --output my_foldseek_db
2024-06-26 06:34:10.655 | INFO     | phold.utils.util:begin_phold:79 - Parameter: --threads 1
2024-06-26 06:34:10.655 | INFO     | phold.utils.util:begin_phold:79 - Parameter: --force False
2024-06-26 06:34:10.655 | INFO     | phold.utils.util:begin_phold:79 - Parameter: --prefix phold_foldseek_db
2024-06-26 06:34:10.853 | INFO     | phold.utils.validation:check_dependencies:117 - Foldseek version found is v8.ef4e960
2024-06-26 06:34:10.853 | INFO     | phold.utils.validation:check_dependencies:126 - Foldseek version is ok
2024-06-26 06:34:10.854 | INFO     | phold:createdb:1048 - Creating the Foldseek database using phold_08_phrogs_train/phold_aa.fasta and phold_08_phrogs_train/phold_3di.fasta.
2024-06-26 06:34:10.854 | INFO     | phold:createdb:1049 - The database will be saved in the my_foldseek_db directory and be called phold_foldseek_db.
2024-06-26 06:34:17.875 | INFO     | phold.utils.external_tools:run:44 - Started running foldseek tsv2db my_foldseek_db/aa.tsv my_foldseek_db/phold_foldseek_db --output-dbtype 0 ...
2024-06-26 06:34:18.378 | INFO     | phold.utils.external_tools:run:46 - Done running foldseek tsv2db my_foldseek_db/aa.tsv my_foldseek_db/phold_foldseek_db --output-dbtype 0
2024-06-26 06:34:18.382 | INFO     | phold.utils.external_tools:run:44 - Started running foldseek tsv2db my_foldseek_db/3di.tsv my_foldseek_db/phold_foldseek_db_ss --output-dbtype 0 ...
2024-06-26 06:34:18.905 | INFO     | phold.utils.external_tools:run:46 - Done running foldseek tsv2db my_foldseek_db/3di.tsv my_foldseek_db/phold_foldseek_db_ss --output-dbtype 0
2024-06-26 06:34:18.909 | INFO     | phold.utils.external_tools:run:44 - Started running foldseek tsv2db my_foldseek_db/header.tsv my_foldseek_db/phold_foldseek_db_h --output-dbtype 12 ...
2024-06-26 06:34:19.195 | INFO     | phold.utils.external_tools:run:46 - Done running foldseek tsv2db my_foldseek_db/header.tsv my_foldseek_db/phold_foldseek_db_h --output-dbtype 12
2024-06-26 06:34:19.347 | INFO     | phold.utils.util:end_phold:101 - phold createdb has finished
2024-06-26 06:34:19.348 | INFO     | phold.utils.util:end_phold:102 - Elapsed time: 8.71 seconds