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2024-03-08 18:52:57,067 - The subcommand ['mmseqs', 'createindex', 'DRAM_data/uniref90.20240308.mmsdb', 'DRAM_data/tmp', '--threads', '10'] experienced an error: Killed
Traceback (most recent call last):
File "/gpfs/fs3c/aafc/aafc_shp/can0002/miniconda3/envs/dram_env/bin/DRAM-setup.py", line 187, in
args.func(**args_dict)
File "/gpfs/fs3c/aafc/aafc_shp/can0002/miniconda3/envs/dram_env/lib/python3.10/site-packages/mag_annotator/database_processing.py", line 615, in prepare_databases
processed_locs = process_functions[i](locs[i], output_dir, LOGGER,
File "/gpfs/fs3c/aafc/aafc_shp/can0002/miniconda3/envs/dram_env/lib/python3.10/site-packages/mag_annotator/database_processing.py", line 322, in process_uniref
make_mmseqs_db(uniref_fasta_zipped, uniref_mmseqs_db, logger, create_index=True, threads=threads, verbose=verbose)
File "/gpfs/fs3c/aafc/aafc_shp/can0002/miniconda3/envs/dram_env/lib/python3.10/site-packages/mag_annotator/utils.py", line 98, in make_mmseqs_db
run_process(['mmseqs', 'createindex', output_loc, tmp_dir, '--threads', str(threads)], logger, verbose=verbose)
File "/gpfs/fs3c/aafc/aafc_shp/can0002/miniconda3/envs/dram_env/lib/python3.10/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 mmseqs createindex DRAM_data/uniref90.20240308.mmsdb DRAM_data/tmp --threads 10 experienced an error, see the log for more info.
The text was updated successfully, but these errors were encountered:
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.
Hi,
I am having problems installing the DRAM database. I get the same error on two different servers. I installed DRAM following the instructions:
git clone https://github.com/WrightonLabCSU/DRAM.git
cd DRAM
conda create --name dram_env -f environment.yaml
conda activate dram_env
Install pip
conda install pip3
pip3 install ./
Here is the error:
2024-03-08 18:16:35,301 - Processing uniref
2024-03-08 18:52:57,067 - The subcommand ['mmseqs', 'createindex', 'DRAM_data/uniref90.20240308.mmsdb', 'DRAM_data/tmp', '--threads', '10'] experienced an error: Killed
Traceback (most recent call last):
File "/gpfs/fs3c/aafc/aafc_shp/can0002/miniconda3/envs/dram_env/bin/DRAM-setup.py", line 187, in
args.func(**args_dict)
File "/gpfs/fs3c/aafc/aafc_shp/can0002/miniconda3/envs/dram_env/lib/python3.10/site-packages/mag_annotator/database_processing.py", line 615, in prepare_databases
processed_locs = process_functions[i](locs[i], output_dir, LOGGER,
File "/gpfs/fs3c/aafc/aafc_shp/can0002/miniconda3/envs/dram_env/lib/python3.10/site-packages/mag_annotator/database_processing.py", line 322, in process_uniref
make_mmseqs_db(uniref_fasta_zipped, uniref_mmseqs_db, logger, create_index=True, threads=threads, verbose=verbose)
File "/gpfs/fs3c/aafc/aafc_shp/can0002/miniconda3/envs/dram_env/lib/python3.10/site-packages/mag_annotator/utils.py", line 98, in make_mmseqs_db
run_process(['mmseqs', 'createindex', output_loc, tmp_dir, '--threads', str(threads)], logger, verbose=verbose)
File "/gpfs/fs3c/aafc/aafc_shp/can0002/miniconda3/envs/dram_env/lib/python3.10/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 mmseqs createindex DRAM_data/uniref90.20240308.mmsdb DRAM_data/tmp --threads 10 experienced an error, see the log for more info.
The text was updated successfully, but these errors were encountered: