Skipping --kofam_hmm_loc works if anyone fails to prepare database for KOfam

[hellopeccat]

I noted an interesting bug relevant to ko_list.gz and its decompressed file kofam_ko_list.tsv.

When I manually downloaded my desired databases, including KOfam, and run prepare database module as follows:
DRAM-setup.py prepare_databases --output_dir /mnt/8T_1/DRAM_db/ --skip_uniref --pfam_loc /mnt/8T_1/DRAM_db/Pfam-A.full.gz --pfam_hmm_dat /mnt/8T_1/DRAM_db/Pfam-A.hmm.dat.gz --kofam_hmm_loc /mnt/8T_1/DRAM_db/profiles.tar.gz --kofam_ko_list_loc /mnt/8T_1/DRAM_db/ko_list.gz --dbcan_loc /mnt/8T_1/DRAM_db/dbCAN-HMMdb-V9.txt --dbcan_fam_activities /mnt/8T_1/DRAM_db/CAZyDB.07302020.fam-activities.txt --vogdb_loc /mnt/8T_1/DRAM_db/vog.hmm.tar.gz --vog_annotations /mnt/8T_1/DRAM_db/vog.annotations.tsv.gz --viral_loc /mnt/8T_1/DRAM_db/viral.1.protein.faa.gz

The kofam succeeded to be processed, however triggered another surprising error

2025-03-11 13:32:33.675820: Database preparation started
0:44:08.388304: PFAM database processed
0:44:10.698177: dbCAN database processed
0:44:26.101377: RefSeq viral database processed
0:48:53.351218: MEROPS database processed
0:50:41.912514: VOGdb database processed
1:02:47.263757: KOfam database processed
1:02:48.296860: KOfam ko list processed
1:02:48.296958: PFAM hmm dat processed
1:02:48.297030: dbCAN fam activities processed
1:02:48.297055: VOGdb annotations processed
1:03:22.357565: DRAM databases and forms downloaded
1:03:22.369840: Files moved to final destination
1:03:22.369994: Setting database paths
Traceback (most recent call last):
  File "/usr/local/software/anaconda3/envs/DRAM/bin/DRAM-setup.py", line 146, in <module>
    args.func(**args_dict)
  File "/usr/local/software/anaconda3/envs/DRAM/lib/python3.6/site-packages/mag_annotator/database_processing.py", line 528, in prepare_databases
    set_database_paths(**output_dbs, use_current_locs=False, update_description_db=True, start_time=start_time)
  File "/usr/local/software/anaconda3/envs/DRAM/lib/python3.6/site-packages/mag_annotator/database_processing.py", line 335, in set_database_paths
    db_dict = check_exists_and_add_to_location_dict(kofam_ko_list_loc, 'kofam_ko_list', db_dict)
  File "/usr/local/software/anaconda3/envs/DRAM/lib/python3.6/site-packages/mag_annotator/database_processing.py", line 305, in check_exists_and_add_to_location_dict
    if check_file_exists(loc):
  File "/usr/local/software/anaconda3/envs/DRAM/lib/python3.6/site-packages/mag_annotator/database_processing.py", line 34, in check_file_exists
    raise ValueError("Database location does not exist: %s" % db_loc)
ValueError: Database location does not exist: /mnt/8T_1/DRAM_db/kofam_ko_list.tsv

At first, I moved the decompressed file, named ko_list to kofam_ko_list.tsv, and made a copy of ko_list.gz to give the argument of --kofam_hmm_loc. However, the program returned
subprocess.CalledProcessError: Command '['gunzip', '/mnt/8T_1/DRAM_db/ko_list.gz']' returned non-zero exit status 2.

I didn't figure out what happened to the command gunzip, but I subsequently skipped to set --kofam_hmm_loc and that worked. Hope this bug fixed soon.