Problem with database instalation (vog_latest_hmms.txt is empty)

[ghost]

I used the following comand to install DRAM database: DRAM-setup.py prepare_databases --skip_uniref --output_dir DRAM_db --threads 40

However I an experiencing problems during instalation with hmmpres. Here is the error message:

/MP_Data/mambaforge/envs/DRAM/lib/python3.11/site-packages/mag_annotator/database_handler.py:126: UserWarning: Database does not exist at path None warnings.warn("Database does not exist at path %s" % description_loc) 2024-04-24 18:48:09,361 - Starting the process of downloading data 2024-04-24 18:48:09,361 - Skipping UniRef 2024-04-24 18:48:09,361 - 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 2024-04-24 18:48:09,361 - 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 2024-04-24 18:48:09,361 - Database preparation started 2024-04-24 18:48:09,361 - Downloading kofam_hmm 2024-04-24 18:51:51,271 - Downloading kofam_ko_list 2024-04-24 18:52:23,996 - Downloading pfam 2024-04-24 19:21:55,420 - Downloading pfam_hmm 2024-04-24 19:21:57,290 - Downloading dbcan 2024-04-24 19:22:06,507 - Downloading dbcan_fam_activities 2024-04-24 19:22:06,507 - Downloading dbCAN family activities from : https://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fam-activities.txt 2024-04-24 19:22:06,915 - Downloading dbcan_subfam_ec 2024-04-24 19:22:06,915 - Downloading dbCAN sub-family encumber from : https://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fam.subfam.ec.txt 2024-04-24 19:22:08,202 - Downloading vogdb 2024-04-24 19:23:24,503 - Downloading vog_annotations 2024-04-24 19:23:25,939 - Downloading viral 2024-04-24 19:24:05,839 - Downloading peptidase 2024-04-24 19:24:51,776 - Downloading genome_summary_form 2024-04-24 19:24:52,166 - Downloading module_step_form 2024-04-24 19:24:52,509 - Downloading function_heatmap_form 2024-04-24 19:24:52,667 - Downloading amg_database 2024-04-24 19:24:52,819 - Downloading etc_module_database 2024-04-24 19:24:53,016 - All raw data files were downloaded successfully 2024-04-24 19:24:53,016 - Processing kofam_hmm 2024-04-24 19:27:08,103 - KOfam database processed 2024-04-24 19:27:08,168 - Moved kofam_hmm to final destination, configuration updated 2024-04-24 19:27:08,168 - Processing kofam_ko_list 2024-04-24 19:27:08,188 - KOfam ko list processed 2024-04-24 19:27:08,189 - Moved kofam_ko_list to final destination, configuration updated 2024-04-24 19:27:08,189 - Processing pfam 2024-04-24 19:50:21,919 - PFAM database processed 2024-04-24 19:50:21,920 - Moved pfam to final destination, configuration updated 2024-04-24 19:50:21,921 - Moved pfam_hmm to final destination, configuration updated 2024-04-24 19:50:21,921 - Processing dbcan 2024-04-24 19:50:23,253 - dbCAN database processed 2024-04-24 19:50:23,259 - Moved dbcan to final destination, configuration updated 2024-04-24 19:50:23,260 - Moved dbcan_fam_activities to final destination, configuration updated 2024-04-24 19:50:23,274 - Moved dbcan_subfam_ec to final destination, configuration updated 2024-04-24 19:50:23,274 - Processing vogdb 2024-04-24 19:50:47,761 - The subcommand ['hmmpress', '-f', 'DRAM_db/vog_latest_hmms.txt'] experienced an error: Error: File format problem in trying to open HMM file DRAM_db/vog_latest_hmms.txt. File exists, but appears to be empty?

Traceback (most recent call last): File "/MP_Data/mambaforge/envs/DRAM/bin/DRAM-setup.py", line 187, in args.func(**args_dict) File "/MP_Data/mambaforge/envs/DRAM/lib/python3.11/site-packages/mag_annotator/database_processing.py", line 615, in prepare_databases processed_locs = process_functions[i](locs[i], output_dir, LOGGER, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/MP_Data/mambaforge/envs/DRAM/lib/python3.11/site-packages/mag_annotator/database_processing.py", line 377, in process_vogdb run_process(['hmmpress', '-f', vog_hmms], logger, verbose=verbose) File "/MP_Data/mambaforge/envs/DRAM/lib/python3.11/site-packages/mag_annotator/utils.py", line 71, in run_process raise subprocess.SubprocessError(f"The subcommand {' '.join(command)} experienced an error, see the log for more info.") subprocess.SubprocessError: The subcommand hmmpress -f DRAM_db/vog_latest_hmms.txt experienced an error, see the log for more info.

[sahilrishav2]

This link has solved the above mentioned issue

https://github.com/WrightonLabCSU/DRAM/issues/340

[BioRRW]

Thank you for choosing to use DRAM. Unfortunately, at this time, we do not have the capacity to provide support for DRAM. We appreciate your understanding and encourage you to stay tuned for the release of DRAM2, expected in 2025.

Best regards, DRAM dev team