BioRRW
commented
1 month ago 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
I have been trying to do a new conda install of DRAM on my server but the prepare_databases step keeps running into an error after downloading all of the raw data. The traceback call suggests it cannot find a file or directory for hmmpress:
2024-02-19 20:35:59,539 - Database preparation started 2024-02-19 20:35:59,539 - Downloading kofam_hmm 2024-02-19 20:38:24,912 - Downloading kofam_ko_list 2024-02-19 20:38:27,909 - Downloading uniref 2024-02-19 21:19:03,749 - Downloading pfam 2024-02-19 21:41:05,368 - Downloading pfam_hmm 2024-02-19 21:41:07,041 - Downloading dbcan 2024-02-19 21:41:32,824 - Downloading dbcan_fam_activities 2024-02-19 21:41:32,825 - Downloading dbCAN family activities from : https://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fam-activities.txt
args.func(*args_dict)
File "/datastore/tools/gregoire/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_processing.py", line 615, in prepare_databases
2024-02-19 21:41:33,050 - Downloading dbcan_subfam_ec 2024-02-19 21:41:33,051 - Downloading dbCAN sub-family encumber from : https://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fam.subfam.ec.txt
2024-02-19 21:41:33,462 - Downloading vogdb 2024-02-19 21:43:04,441 - Downloading vog_annotations 2024-02-19 21:43:05,611 - Downloading viral 2024-02-19 21:43:45,762 - Downloading peptidase 2024-02-19 21:44:57,862 - Downloading genome_summary_form 2024-02-19 21:44:58,130 - Downloading module_step_form 2024-02-19 21:44:58,382 - Downloading function_heatmap_form 2024-02-19 21:44:58,551 - Downloading amg_database 2024-02-19 21:44:58,722 - Downloading etc_module_database 2024-02-19 21:44:58,877 - All raw data files were downloaded successfully 2024-02-19 21:44:58,877 - Processing kofam_hmm Traceback (most recent call last): File "/datastore/tools/gregoire/envs/DRAM/bin/DRAM-setup.py", line 187, in
processed_locs = process_functions[i](locs[i], output_dir, LOGGER, File "/datastore/tools/gregoire/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_processing.py", line 246, in process_kofam_hmm
run_process(['hmmpress', '-f', merged_kofam_profiles], logger, verbose=verbose) File "/datastore/tools/gregoire/envs/DRAM/lib/python3.10/site-packages/mag_annotator/utils.py", line 61, in run_process results = subprocess.run(command, check=check, shell=shell, File "/datastore/tools/gregoire/envs/DRAM/lib/python3.10/subprocess.py", line 503, in run with Popen(popenargs, **kwargs) as process: File "/datastore/tools/gregoire/envs/DRAM/lib/python3.10/subprocess.py", line 971, in init self._execute_child(args, executable, preexec_fn, close_fds, File "/datastore/tools/gregoire/envs/DRAM/lib/python3.10/subprocess.py", line 1863, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'hmmpress'
I double checked that hmmpress is in the environment with 'which hmmpress' and it returns that it is in the DRAM environment
/datastore/tools/gregoire/envs/DRAM/bin/hmmpressI am not sure how to address this or whether this stems from edits I had to make to the environmental.yaml to get the initial DRAM environment created properly with mamba to begin with following this post : https://github.com/WrightonLabCSU/DRAM/issues/330