Continue the "prepare_database" process

[chenyj8]

Hi developer,

I aim to set up the database, but the network connection issue stops the process. Is there a way to continue the "prepare_databases" process without starting everything over?

My command is:

DRAM-setup.py prepare_databases --threads 10 --output_dir /groups/chenyj/db/dram/

Please see below the log file:

2024-02-21 17:58:27,555 - Starting the process of downloading data 2024-02-21 17:58:27,555 - The kegg_loc argument was not used to specify a downloaded kegg file, and dram can not download it its self. So it is assumed that the user wants to set up DRAM without it 2024-02-21 17:58:27,555 - The gene_ko_link_loc argument was not used to specify a downloaded gene_ko_link file, and dram can not download it its self. So it is assumed that the user wants to set up DRAM without it 2024-02-21 17:58:27,555 - Database preparation started 2024-02-21 17:58:27,555 - Downloading kofam_hmm 2024-02-21 23:40:49,402 - Downloading kofam_ko_list 2024-02-21 23:41:01,398 - Downloading uniref 2024-02-22 12:48:47,083 - Downloading pfam 2024-02-23 03:51:14,104 - Downloading pfam_hmm 2024-02-23 03:51:17,102 - Downloading dbcan 2024-02-23 04:09:15,738 - Downloading dbcan_fam_activities 2024-02-23 04:09:15,738 - Downloading dbCAN family activities from : https://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fam-activities.txt 2024-02-23 04:09:17,025 - Downloading dbcan_subfam_ec 2024-02-23 04:09:17,025 - Downloading dbCAN sub-family encumber from : https://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fam.subfam.ec.txt 2024-02-23 04:09:27,129 - Downloading vogdb 2024-02-23 04:12:58,907 - Downloading vog_annotations 2024-02-23 04:13:00,947 - Downloading viral 2024-02-23 04:14:00,457 - Downloading peptidase 2024-02-23 04:17:19,469 - Downloading genome_summary_form 2024-02-23 04:17:19,476 - Something went wrong with the download of the url: https://raw.githubusercontent.com/WrightonLabCSU/DRAM/master/data/genome_summary_form.tsv 2024-02-23 04:17:19,476 - <urlopen error [Errno 111] Connection refused>

Please see below the DRAM database folder:

Best,

Yongjian

[SwapnilDoijad]

+1 for the above request. Updating the script to skip already downloaded/installed databases would be helpful.

[jianshu93]

Also have the same problem here, the viral model is kind of buggy but I have to rebuild the whole database, which I really do not want to.

Jianshu