Oui,
je lance le code avec la commande sbatch my_fold_mult.sh
le code est:
#!/bin/bash
#
#SBATCH -A tfheterodimer_3dpred
#SBATCH -p gpu
#SBATCH --gres=gpu:1g.5gb:1
#SBATCH --cpus-per-task=10
#SBATCH --mem=50G
module load alphafold/2.2.3
mkdir -p /tmp/$USER_alphafold
srun run_alphafold.sh --fasta_paths=/shared/home/rblanc/tests/AlphaFold/LFY_UFO.fasta \
--output_dir=/shared/projects/tfheterodimer_3dpred/AlphaFold \
--model_preset=multimer \
--db_preset=full_dbs \
--data_dir=/shared/bank/alphafold2/current \
--uniref90_database_path=/shared/bank/alphafold2/current/uniref90/uniref90.fasta \
--mgnify_database_path=/shared/bank/alphafold2/current/mgnify/mgy_clusters_2018_12.fa \
--template_mmcif_dir=/shared/bank/alphafold2/current/pdb_mmcif/mmcif_files \
--max_template_date=2020-05-14 \
--obsolete_pdbs_path=/shared/bank/alphafold2/current/pdb_mmcif/obsolete.dat \
--bfd_database_path=/shared/bank/alphafold2/current/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
--uniclust30_database_path=/shared/bank/alphafold2/current/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
--use_gpu_relax=1 \
--pdb_seqres_database_path=/shared/bank/alphafold2/current/pdb_seqres \
--uniprot_database_path=/shared/bank/alphafold2/current/uniprot
et l'erreur complète est:
I1208 12:50:17.492459 47972528590528 templates.py:857] Using precomputed obsolete pdbs /shared/bank/alphafold2/current/pdb_mmcif/obsolete.dat.
I1208 12:50:18.265425 47972528590528 tpu_client.py:54] Starting the local TPU driver.
I1208 12:50:18.375782 47972528590528 xla_bridge.py:212] Unable to initialize backend 'tpu_driver': Not found: Unable to find driver in registry given worker: local://
I1208 12:50:19.362817 47972528590528 xla_bridge.py:212] Unable to initialize backend 'tpu': Invalid argument: TpuPlatform is not available.
I1208 12:50:22.875974 47972528590528 run_alphafold.py:376] Have 25 models: ['model_1_multimer_v2_pred_0', 'model_1_multimer_v2_pred_1', 'model_1_multimer_v2_pred_2', '
model_1_multimer_v2_pred_3', 'model_1_multimer_v2_pred_4', 'model_2_multimer_v2_pred_0', 'model_2_multimer_v2_pred_1', 'model_2_multimer_v2_pred_2', 'model_2_multimer_
v2_pred_3', 'model_2_multimer_v2_pred_4', 'model_3_multimer_v2_pred_0', 'model_3_multimer_v2_pred_1', 'model_3_multimer_v2_pred_2', 'model_3_multimer_v2_pred_3', 'mode
l_3_multimer_v2_pred_4', 'model_4_multimer_v2_pred_0', 'model_4_multimer_v2_pred_1', 'model_4_multimer_v2_pred_2', 'model_4_multimer_v2_pred_3', 'model_4_multimer_v2_p
red_4', 'model_5_multimer_v2_pred_0', 'model_5_multimer_v2_pred_1', 'model_5_multimer_v2_pred_2', 'model_5_multimer_v2_pred_3', 'model_5_multimer_v2_pred_4']
I1208 12:50:22.876127 47972528590528 run_alphafold.py:393] Using random seed 8481300240475865 for the data pipeline
I1208 12:50:22.876272 47972528590528 run_alphafold.py:161] Predicting LFY_UFO
I1208 12:50:22.882764 47972528590528 pipeline_multimer.py:210] Running monomer pipeline on chain A: sp|Q00958|LFY_ARATH Protein LEAFY OS=Arabidopsis thaliana OX=3702 G
N=LFY PE=1 SV=2
I1208 12:50:22.882892 47972528590528 jackhmmer.py:133] Launching subprocess "/shared/ifbstor1/software/miniconda/envs/alphafold-2.2.3/bin/jackhmmer -o /dev/null -A /tm
p/tmpgqarqlop/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 /tmp/tmpmlv03i3c.fasta /shared/bank/alphafold2/current/uniref90
/uniref90.fasta"
I1208 12:50:22.911369 47972528590528 utils.py:36] Started Jackhmmer (uniref90.fasta) query
I1208 12:57:00.120888 47972528590528 utils.py:40] Finished Jackhmmer (uniref90.fasta) query in 397.209 seconds
I1208 12:57:00.135301 47972528590528 jackhmmer.py:133] Launching subprocess "/shared/ifbstor1/software/miniconda/envs/alphafold-2.2.3/bin/jackhmmer -o /dev/null -A /tm
p/tmpghsvvxfe/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 /tmp/tmpmlv03i3c.fasta /shared/bank/alphafold2/current/mgnify/m
gy_clusters_2018_12.fa"
I1208 12:57:00.146211 47972528590528 utils.py:36] Started Jackhmmer (mgy_clusters_2018_12.fa) query
I1208 13:01:44.694318 47972528590528 utils.py:40] Finished Jackhmmer (mgy_clusters_2018_12.fa) query in 284.506 seconds
I1208 13:01:45.024384 47972528590528 hmmbuild.py:121] Launching subprocess ['/shared/ifbstor1/software/miniconda/envs/alphafold-2.2.3/bin/hmmbuild', '--hand', '--amino
', '/tmp/tmp_ypfr_ks/output.hmm', '/tmp/tmp_ypfr_ks/query.msa']
I1208 13:01:45.080546 47972528590528 utils.py:36] Started hmmbuild query
I1208 13:01:45.510279 47972528590528 hmmbuild.py:128] hmmbuild stdout:
# hmmbuild :: profile HMM construction from multiple sequence alignments
# HMMER 3.3.2 (Nov 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# input alignment file: /tmp/tmp_ypfr_ks/query.msa
# output HMM file: /tmp/tmp_ypfr_ks/output.hmm
# input alignment is asserted as: protein
# model architecture construction: hand-specified by RF annotation
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# idx name nseq alen mlen eff_nseq re/pos description
#---- -------------------- ----- ----- ----- -------- ------ -----------
1 query 593 1232 420 3.16 0.590
# CPU time: 0.42u 0.00s 00:00:00.42 Elapsed: 00:00:00.42
stderr:
I1208 13:01:45.510342 47972528590528 utils.py:40] Finished hmmbuild query in 0.429 seconds
I1208 13:01:45.511947 47972528590528 hmmsearch.py:103] Launching sub-process ['/shared/ifbstor1/software/miniconda/envs/alphafold-2.2.3/bin/hmmsearch', '--noali', '--c
pu', '8', '--F1', '0.1', '--F2', '0.1', '--F3', '0.1', '--incE', '100', '-E', '100', '--domE', '100', '--incdomE', '100', '-A', '/tmp/tmppjrtdui6/output.sto', '/tmp/tm
ppjrtdui6/query.hmm', '/shared/bank/alphafold2/current/pdb_seqres']
I1208 13:01:45.539009 47972528590528 utils.py:36] Started hmmsearch (pdb_seqres) query
I1208 13:01:45.546266 47972528590528 utils.py:40] Finished hmmsearch (pdb_seqres) query in 0.007 seconds
Traceback (most recent call last):
File "/shared/ifbstor1/software/miniconda/envs/alphafold-2.2.3/bin/run_alphafold.py", line 422, in <module>
app.run(main)
File "/shared/ifbstor1/software/miniconda/envs/alphafold-2.2.3/lib/python3.8/site-packages/absl/app.py", line 312, in run
_run_main(main, args)
File "/shared/ifbstor1/software/miniconda/envs/alphafold-2.2.3/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main
sys.exit(main(argv))
File "/shared/ifbstor1/software/miniconda/envs/alphafold-2.2.3/bin/run_alphafold.py", line 398, in main
predict_structure(
File "/shared/ifbstor1/software/miniconda/envs/alphafold-2.2.3/bin/run_alphafold.py", line 172, in predict_structure
feature_dict = data_pipeline.process(
File "/shared/ifbstor1/software/miniconda/envs/alphafold-2.2.3/lib/python3.8/site-packages/alphafold/data/pipeline_multimer.py", line 264, in process
chain_features = self._process_single_chain(
File "/shared/ifbstor1/software/miniconda/envs/alphafold-2.2.3/lib/python3.8/site-packages/alphafold/data/pipeline_multimer.py", line 212, in _process_single_chain
chain_features = self._monomer_data_pipeline.process(
File "/shared/ifbstor1/software/miniconda/envs/alphafold-2.2.3/lib/python3.8/site-packages/alphafold/data/pipeline.py", line 185, in process
pdb_templates_result = self.template_searcher.query(msa_for_templates)
File "/shared/ifbstor1/software/miniconda/envs/alphafold-2.2.3/lib/python3.8/site-packages/alphafold/data/tools/hmmsearch.py", line 79, in query
return self.query_with_hmm(hmm)
File "/shared/ifbstor1/software/miniconda/envs/alphafold-2.2.3/lib/python3.8/site-packages/alphafold/data/tools/hmmsearch.py", line 112, in query_with_hmm
raise RuntimeError(
RuntimeError: hmmsearch failed:
stdout:
stderr:
Fatal exception (source file esl_buffer.c, line 1608):
failed to slurp /shared/bank/alphafold2/current/pdb_seqres
srun: error: gpu-node-01: task 0: Exited with exit code 1