Error setting up databases DRAM_data/tmp/10969822372036018711/createindex.sh: line 56: 1115772 Killed

[ileleiwi]

Hello,

I'm having difficulty setting up the databases for DRAM on the server I'm using. The command I'm running is

DRAM-setup.py prepare_databases --output_dir DRAM_data --uniref_loc /global/cfs/cdirs/m3264/databases/dram_database_files/uniref90.fasta.gz --vogdb_loc /global/cfs/cdirs/m3264/databases/dram_database_files/vog.hmm.tar.gz --pfam_loc /global/cfs/cdirs/m3264/databases/dram_database_files/Pfam-A.full.gz --verbose

The output I receive is as follows:

/global/homes/l/leleiwi1/.conda/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_handler.py:123: UserWarning: Database does not exist at path None
  warnings.warn("Database does not exist at path %s" % description_loc)
2023-12-06 09:17:24,802 - Starting the process of downloading data
2023-12-06 09:17:24,829 - 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
2023-12-06 09:17:24,829 - 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
2023-12-06 09:17:24,829 - Database preparation started
2023-12-06 09:17:24,829 - Downloading kofam_hmm
downloading ftp://ftp.genome.jp/pub/db/kofam/profiles.tar.gz
2023-12-06 09:22:29,886 - Downloading kofam_ko_list
downloading ftp://ftp.genome.jp/pub/db/kofam/ko_list.gz
2023-12-06 09:22:35,761 - Downloading pfam_hmm
downloading ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.dat.gz
2023-12-06 09:22:38,585 - Downloading dbcan
downloading http://bcb.unl.edu/dbCAN2/download/dbCAN-HMMdb-V11.txt
2023-12-06 09:22:40,827 - Downloading dbcan_fam_activities
2023-12-06 09:22:40,827 - Downloading dbCAN family activities from : https://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fam-activities.txt
downloading https://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fam-activities.txt
2023-12-06 09:22:41,084 - Downloading dbcan_subfam_ec
2023-12-06 09:22:41,084 - Downloading dbCAN sub-family encumber from : https://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fam.subfam.ec.txt
downloading https://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fam.subfam.ec.txt
2023-12-06 09:22:41,500 - Downloading vog_annotations
downloading http://fileshare.csb.univie.ac.at/vog/latest/vog.annotations.tsv.gz
2023-12-06 09:22:45,785 - Downloading viral
downloading ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.1.protein.faa.gz
2023-12-06 09:22:48,877 - Downloading peptidase
downloading ftp://ftp.ebi.ac.uk/pub/databases/merops/current_release/pepunit.lib
2023-12-06 09:22:55,874 - Downloading genome_summary_form
downloading https://raw.githubusercontent.com/WrightonLabCSU/DRAM/master/data/genome_summary_form.tsv
2023-12-06 09:22:56,179 - Downloading module_step_form
downloading https://raw.githubusercontent.com/WrightonLabCSU/DRAM/master/data/module_step_form.tsv
2023-12-06 09:22:56,580 - Downloading function_heatmap_form
downloading https://raw.githubusercontent.com/WrightonLabCSU/DRAM/master/data/function_heatmap_form.tsv
2023-12-06 09:22:56,769 - Downloading amg_database
downloading https://raw.githubusercontent.com/WrightonLabCSU/DRAM/master/data/amg_database.tsv
2023-12-06 09:22:56,938 - Downloading etc_module_database
downloading https://raw.githubusercontent.com/WrightonLabCSU/DRAM/master/data/etc_module_database.tsv
2023-12-06 09:22:57,132 - All raw data files were downloaded successfully
2023-12-06 09:22:57,132 - Processing uniref
2023-12-06 10:00:26,828 - The subcommand ['mmseqs', 'createindex', 'DRAM_data/uniref90.20231206.mmsdb', 'DRAM_data/tmp', '--threads', '10'] experienced an error: DRAM_data/tmp/10969822372036018711/createindex.sh: line 56: 1115772 Killed                  "$MMSEQS" $INDEXER "$INPUT" "$INPUT" ${INDEX_PAR}

Traceback (most recent call last):
  File "/global/homes/l/leleiwi1/.conda/envs/DRAM/bin/DRAM-setup.py", line 184, in <module>
    args.func(**args_dict)
  File "/global/homes/l/leleiwi1/.conda/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_processing.py", line 555, in prepare_databases
    processed_locs = process_functions[i](locs[i], output_dir, LOGGER,
  File "/global/homes/l/leleiwi1/.conda/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_processing.py", line 262, in process_uniref
    make_mmseqs_db(uniref_fasta_zipped, uniref_mmseqs_db, logger, create_index=True, threads=threads, verbose=verbose)
  File "/global/homes/l/leleiwi1/.conda/envs/DRAM/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 "/global/homes/l/leleiwi1/.conda/envs/DRAM/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/uniref90.20231206.mmsdb DRAM_data/tmp --threads 10 experienced an error, see the log for more info.

Do you know why this is happening and can you help me solve the problem? I'm running in a conda environment with DRAM version 1.4.6. The databases all seem to download fine, it's just this processing step with mmseqs2.
I noticed that the DRAM_data/tmp/10969822372036018711/createindex.sh file referenced in the error is made with the following file permisions -rwx------.
I thought it could be a file permission problem since line 56 is the last line of that file. However, when I change the permisions of the file and try to run bash DRAM_data/tmp/10969822372036018711/createindex.sh I'm prompted with this output Please provide <sequenceDB> <tmp> and there seems to be no way to restart the original command when the DRAM_data folder already exists.

Thanks for your help,
Kai