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Description
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.
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