Multimer 8 killed python /app/alphafold/run_alphafold.py "$@"

[Justice-Lu]

I0322 10:43:41.310137 140522693193920 run_docker.py:258] I0322 14:43:41.309186 140233224365888 pipeline.py:235] BFD MSA size: 7266 sequences.
I0322 10:43:41.310351 140522693193920 run_docker.py:258] I0322 14:43:41.309243 140233224365888 pipeline.py:236] MGnify MSA size: 501 sequences.
I0322 10:43:41.331412 140522693193920 run_docker.py:258] I0322 14:43:41.309300 140233224365888 pipeline.py:237] Final (deduplicated) MSA size: 15775 sequences.
I0322 10:43:41.339361 140522693193920 run_docker.py:258] I0322 14:43:41.309364 140233224365888 pipeline.py:239] Total number of templates (NB: this can include bad templates and is later filtered to top 4): 20.
I0322 10:43:41.525612 140522693193920 run_docker.py:258] I0322 14:43:41.414972 140233224365888 jackhmmer.py:133] Launching subprocess "/usr/bin/jackhmmer -o /dev/null -A /tmp/tmpf3w8h8wj/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 /tmp/tmph25gr5sx.fasta /mnt/uniprot_database_path/uniprot.fasta"
I0322 10:43:41.864998 140522693193920 run_docker.py:258] I0322 14:43:41.864015 140233224365888 utils.py:36] Started Jackhmmer (uniprot.fasta) query
I0322 11:23:17.895058 140522693193920 run_docker.py:258] I0322 15:23:13.848875 140233224365888 utils.py:40] Finished Jackhmmer (uniprot.fasta) query in 2371.977 seconds
I0322 11:31:56.784576 140522693193920 run_docker.py:258] /app/run_alphafold.sh: line 3:     8 Killed                  python /app/alphafold/run_alphafold.py "$@"

This following error was observed when running alphafold multimer. I've successfully run alphafold multimer with same script but for different fasta file.

Has anyone seen this kind of error and is there any useful information for solving or knowing what causes this ??

Any information is greatly appreciated. I've included some information of the script and files ran below.

Script used

python3 alphafold2/alphafold/docker/run_docker.py \
  --fasta_paths=./PATH/Multimer_fasta/Rpgf2_Kpct.fasta \
  --max_template_date=2023-01-01 \
  --model_preset=multimer \
  --data_dir=alphafold2/GENDATABASE \
  --output_dir=./PATH/AF_output/ \
--num_multimer_predictions_per_model=1

Multimer fasta (Converted to txt for upload purpose) Rpgf2_Kpct.txt

[FelixHomma]

Not sure if this is still needed, but I got this error before when I ran out of memory. I think it usually happened when the database searches for uniprot.fasta resulted in large msas. Increasing memory (if possible) usually fixes this problem for me.