その後、GPUを使わないオプションの与え方がわかったので、やってみたのだが、やはり走りきらない。
$ nohup python3 docker/run_docker.py --fasta_paths=${HOME}/test5.fasta --max_template_date=2021-08-21 --gpu_devices=none > nohup1.out &
[1] 24564
$ nohup: 標準入力を無視し、標準エラー出力を標準出力にリダイレクトします
[1]+ 終了 nohup python3 docker/run_docker.py --fasta_paths=${HOME}/test5.fasta --max_template_date=2021-08-21 --gpu_devices=none > nohup1.out$ less nohup1.out
$ less nohup1.out
I0822 16:54:19.720113 140334027720512 run_docker.py:119] Mounting /home/kuro -> /mnt/fasta_path_0
I0822 16:54:19.720278 140334027720512 run_docker.py:119] Mounting /mnt/HDD2/af_database/uniref90 -> /mnt/uniref90_database_path
I0822 16:54:19.720366 140334027720512 run_docker.py:119] Mounting /mnt/HDD2/af_database/mgnify -> /mnt/mgnify_database_path
I0822 16:54:19.720427 140334027720512 run_docker.py:119] Mounting /mnt/HDD2/af_database/pdb70 -> /mnt/pdb70_database_path
I0822 16:54:19.720480 140334027720512 run_docker.py:119] Mounting /mnt/HDD2 -> /mnt/data_dir
I0822 16:54:19.720530 140334027720512 run_docker.py:119] Mounting /mnt/HDD2/af_database/pdb_mmcif -> /mnt/template_mmcif_dir
I0822 16:54:19.720584 140334027720512 run_docker.py:119] Mounting /mnt/HDD2/af_database/pdb_mmcif -> /mnt/obsolete_pdbs_path
I0822 16:54:19.720635 140334027720512 run_docker.py:119] Mounting /mnt/HDD2/af_database/uniclust30/uniclust30_2018_08 -> /mnt/uniclust30_database_path
I0822 16:54:19.720705 140334027720512 run_docker.py:119] Mounting /mnt/HDD2/af_database/bfd -> /mnt/bfd_database_path
I0822 16:54:22.553266 140334027720512 run_docker.py:193] /opt/conda/lib/python3.7/site-packages/absl/flags/_validators.py:206: UserWarning: Flag --preset has a non-None default value; therefore, mark_flag_as_required will pass even if flag is not specified in the command line!
I0822 16:54:22.553490 140334027720512 run_docker.py:193] 'command line!' % flag_name)
I0822 16:54:22.937656 140334027720512 run_docker.py:193] I0822 07:54:22.937008 140686220801856 templates.py:836] Using precomputed obsolete pdbs /mnt/obsolete_pdbs_path/obsolete.dat.
I0822 16:54:23.115177 140334027720512 run_docker.py:193] I0822 07:54:23.114689 140686220801856 xla_bridge.py:236] Unable to initialize backend 'tpu_driver': Not found: Unable to find driver in registry given worker:
I0822 16:54:23.119515 140334027720512 run_docker.py:193] 2021-08-22 07:54:23.119223: E external/org_tensorflow/tensorflow/stream_executor/cuda/cuda_driver.cc:271] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected
I0822 16:54:23.119714 140334027720512 run_docker.py:193] I0822 07:54:23.119376 140686220801856 xla_bridge.py:236] Unable to initialize backend 'gpu': Failed precondition: No visible GPU devices.
I0822 16:54:23.120119 140334027720512 run_docker.py:193] I0822 07:54:23.119770 140686220801856 xla_bridge.py:236] Unable to initialize backend 'tpu': Invalid argument: TpuPlatform is not available.
I0822 16:54:23.120244 140334027720512 run_docker.py:193] W0822 07:54:23.119888 140686220801856 xla_bridge.py:240] No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.)
I0822 16:54:29.104912 140334027720512 run_docker.py:193] I0822 07:54:29.104286 140686220801856 run_alphafold.py:268] Have 5 models: ['model_1', 'model_2', 'model_3', 'model_4', 'model_5']
I0822 16:54:29.105086 140334027720512 run_docker.py:193] I0822 07:54:29.104456 140686220801856 run_alphafold.py:280] Using random seed 6136641256249677066 for the data pipeline
I0822 16:54:29.106145 140334027720512 run_docker.py:193] I0822 07:54:29.105848 140686220801856 jackhmmer.py:130] Launching subprocess "/usr/bin/jackhmmer -o /dev/null -A /tmp/tmp34j59llv/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 /mnt/fasta_path_0/test5.fasta /mnt/uniref90_database_path/uniref90.fasta"
I0822 16:54:29.191782 140334027720512 run_docker.py:193] I0822 07:54:29.191061 140686220801856 utils.py:36] Started Jackhmmer (uniref90.fasta) query
I0822 17:01:49.737192 140334027720512 run_docker.py:193] I0822 08:01:49.735362 140686220801856 utils.py:40] Finished Jackhmmer (uniref90.fasta) query in 440.544 seconds
I0822 17:01:49.815391 140334027720512 run_docker.py:193] I0822 08:01:49.814917 140686220801856 jackhmmer.py:130] Launching subprocess "/usr/bin/jackhmmer -o /dev/null -A /tmp/tmp1we8kg9q/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 /mnt/fasta_path_0/test5.fasta /mnt/mgnify_database_path/mgy_clusters_2018_12.fa"
I0822 17:01:49.882002 140334027720512 run_docker.py:193] I0822 08:01:49.881391 140686220801856 utils.py:36] Started Jackhmmer (mgy_clusters_2018_12.fa) query
I0822 17:09:32.012735 140334027720512 run_docker.py:193] I0822 08:09:32.011906 140686220801856 utils.py:40] Finished Jackhmmer (mgy_clusters_2018_12.fa) query in 462.130 seconds
I0822 17:09:34.619096 140334027720512 run_docker.py:193] I0822 08:09:34.618561 140686220801856 hhsearch.py:76] Launching subprocess "/usr/bin/hhsearch -i /tmp/tmp2hwa2yuo/query.a3m -o /tmp/tmp2hwa2yuo/output.hhr -maxseq 1000000 -d /mnt/pdb70_database_path/pdb70"
I0822 17:09:34.720823 140334027720512 run_docker.py:193] I0822 08:09:34.720173 140686220801856 utils.py:36] Started HHsearch query
I0822 17:09:34.993415 140334027720512 run_docker.py:193] I0822 08:09:34.992822 140686220801856 utils.py:40] Finished HHsearch query in 0.272 seconds
I0822 17:09:34.995354 140334027720512 run_docker.py:193] Traceback (most recent call last):
I0822 17:09:34.995493 140334027720512 run_docker.py:193] File "/app/alphafold/run_alphafold.py", line 310, in <module>
I0822 17:09:34.995615 140334027720512 run_docker.py:193] app.run(main)
I0822 17:09:34.995697 140334027720512 run_docker.py:193] File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 312, in run
I0822 17:09:34.995767 140334027720512 run_docker.py:193] _run_main(main, args)
I0822 17:09:34.995833 140334027720512 run_docker.py:193] File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 258, in _run_main
I0822 17:09:34.995898 140334027720512 run_docker.py:193] sys.exit(main(argv))
I0822 17:09:34.995963 140334027720512 run_docker.py:193] File "/app/alphafold/run_alphafold.py", line 292, in main
I0822 17:09:34.996028 140334027720512 run_docker.py:193] random_seed=random_seed)
I0822 17:09:34.996093 140334027720512 run_docker.py:193] File "/app/alphafold/run_alphafold.py", line 129, in predict_structure
I0822 17:09:34.996158 140334027720512 run_docker.py:193] msa_output_dir=msa_output_dir)
I0822 17:09:34.996222 140334027720512 run_docker.py:193] File "/app/alphafold/alphafold/data/pipeline.py", line 140, in process
I0822 17:09:34.996285 140334027720512 run_docker.py:193] hhsearch_result = self.hhsearch_pdb70_runner.query(uniref90_msa_as_a3m)
I0822 17:09:34.996349 140334027720512 run_docker.py:193] File "/app/alphafold/alphafold/data/tools/hhsearch.py", line 87, in query
I0822 17:09:34.996413 140334027720512 run_docker.py:193] stdout.decode('utf-8'), stderr[:100_000].decode('utf-8')))
I0822 17:09:34.996477 140334027720512 run_docker.py:193] RuntimeError: HHSearch failed:
I0822 17:09:34.996541 140334027720512 run_docker.py:193] stdout:
I0822 17:09:34.996605 140334027720512 run_docker.py:193]
I0822 17:09:34.996669 140334027720512 run_docker.py:193]
I0822 17:09:34.996741 140334027720512 run_docker.py:193] stderr:
I0822 17:09:34.996806 140334027720512 run_docker.py:193] - 08:09:34.905 INFO: /tmp/tmp2hwa2yuo/query.a3m is in A2M, A3M or FASTA format
I0822 17:09:34.996870 140334027720512 run_docker.py:193]
I0822 17:09:34.996934 140334027720512 run_docker.py:193] - 08:09:34.906 WARNING: Ignoring invalid symbol '*' at pos. 492 in line 2 of /tmp/tmp2hwa2yuo/query.a3m
I0822 17:09:34.996998 140334027720512 run_docker.py:193]
I0822 17:09:34.997061 140334027720512 run_docker.py:193] - 08:09:34.986 ERROR: [subseq from] Endoglucanase (Fragment) n=2 Tax=Citrus unshiu TaxID=55188 RepID=A0A2H5PNG1_CITUN
I0822 17:09:34.997125 140334027720512 run_docker.py:193] - 08:09:34.986 ERROR: Error in /tmp/hh-suite/src/hhalignment.cpp:1244: Compress:
I0822 17:09:34.997188 140334027720512 run_docker.py:193]
I0822 17:09:34.997251 140334027720512 run_docker.py:193] - 08:09:34.986 ERROR: sequences in /tmp/tmp2hwa2yuo/query.a3m do not all have the same number of columns,
I0822 17:09:34.997315 140334027720512 run_docker.py:193]
I0822 17:09:34.997379 140334027720512 run_docker.py:193] - 08:09:34.986 ERROR:
I0822 17:09:34.997443 140334027720512 run_docker.py:193] e.g. first sequence and sequence UniRef90_A0A2H5PNG1/69-549.
I0822 17:09:34.997507 140334027720512 run_docker.py:193]
I0822 17:09:34.997571 140334027720512 run_docker.py:193] - 08:09:34.986 ERROR: Check input format for '-M a2m' option and consider using '-M first' or '-M 50'
I0822 17:09:34.997642 140334027720512 run_docker.py:193]
I0822 17:09:34.997712 140334027720512 run_docker.py:193]
I0822 17:09:34.997777 140334027720512 run_docker.py:193]
