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WrightonLabCSU / DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
GNU General Public License v3.0
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DRAM database installation problem; The subcommand mmseqs createindex DRAM_data/uniref90.20240308.mmsdb DRAM_data/tmp --threads 10 experienced an error #336

Open camillaln opened 3 months ago

camillaln commented 3 months ago

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.

crane90 commented 2 months ago

i have the same problem when setting up the databases on our Linux cluster. I used this code:

<DRAM-setup.py prepare_databases --output_dir DRAM_data>

and get this error in the log file:

2024-04-02 14:26:39,079 - Downloading function_heatmap_form 2024-04-02 14:26:39,294 - Downloading amg_database 2024-04-02 14:26:39,524 - Downloading etc_module_database 2024-04-02 14:26:39,749 - All raw data files were downloaded successfully 2024-04-02 14:26:39,749 - Processing kofam_hmm 2024-04-02 14:30:15,372 - KOfam database processed 2024-04-02 14:30:16,640 - Moved kofam_hmm to final destination, configuration updated 2024-04-02 14:30:16,640 - Processing kofam_ko_list 2024-04-02 14:30:16,723 - KOfam ko list processed 2024-04-02 14:30:16,726 - Moved kofam_ko_list to final destination, configuration updated 2024-04-02 14:30:16,726 - Processing uniref 2024-04-02 15:19:14,992 - The subcommand ['mmseqs', 'createindex', 'db/DRAM_new/uniref90.20240402.mmsdb', 'db/DRAM_new/tmp', '--threads', '10'] experienced an error: db/DRAM_new/tmp/11412079875784970340/createindex.sh: line 56: 412650 Killed "$MMSEQS" $INDEXER "$INPUT" "$INPUT" ${INDEX_PAR}

crane90 commented 2 months ago

in my case it seems to have run out of working memory, now that i have allocated more working memory for the command it worked fine

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