Error running alphafold #33
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Hi, I am having trouble reproducing this error. Jackhmmer will create a "tmp" folder in your home directory where it will temporarily store downloaded database chunks and then delete them. It looks like one of the database chunks was already deleted before the 'os.remove()' command. I am not sure how this happened. Does it happen every time you run alphafold? |
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Yes this repeatedly happens. Could it be a property of the VM? |
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Do you think it could be because the AA input is too big? I am trying your test sequence from example, and it is running, but very slowly: 173 unique sequences found in total for sequence 1 Running model_1: 0%| | 0/7 [elapsed: 00:00 remaining: ?]Thu Aug 18 15:30:37 2022 WARNING No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.) [Compiling module jit_apply_fn.5] Very slow compile? If you want to file a bug, run with envvar XLA_FLAGS=--xla_dump_to=/tmp/foo and attach the results. 2022-08-18 15:42:51.437904: E external/org_tensorflow/tensorflow/compiler/xla/service/slow_operation_alarm.cc:133] The operation took 7m16.29072564s [Compiling module jit_apply_fn.5] Very slow compile? If you want to file a bug, run with envvar XLA_FLAGS=--xla_dump_to=/tmp/foo and attach the results. /home/ccadmin/anaconda3/envs/gget/lib/python3.9/site-packages/alphafold/model/model.py:172: FutureWarning: jax.tree_map is deprecated, and will be removed in a future release. Use jax.tree_util.tree_map instead. [Compiling module jit_apply_fn.7] Very slow compile? If you want to file a bug, run with envvar XLA_FLAGS=--xla_dump_to=/tmp/foo and attach the results. Running model_3: 29%|██████████████████ | 2/7 [elapsed: 49:08 remaining: 2:02:28] |
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Can confirm short test sequence finished running without a problem: gget alphafold MAAHKGAEHHHKAAEHHEQAAKHHHAAAEHHEKGEHEQAAHHADTAYAHHKHAEEHAAQAAKHDAEHHAPKPH 173 unique sequences found in total for sequence 1 Running model_1: 0%| | 0/7 [elapsed: 00:00 remaining: ?]Thu Aug 18 15:30:37 2022 WARNING No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.) [Compiling module jit_apply_fn.5] Very slow compile? If you want to file a bug, run with envvar XLA_FLAGS=--xla_dump_to=/tmp/foo and attach the results. 2022-08-18 15:42:51.437904: E external/org_tensorflow/tensorflow/compiler/xla/service/slow_operation_alarm.cc:133] The operation took 7m16.29072564s [Compiling module jit_apply_fn.5] Very slow compile? If you want to file a bug, run with envvar XLA_FLAGS=--xla_dump_to=/tmp/foo and attach the results. /home/ccadmin/anaconda3/envs/gget/lib/python3.9/site-packages/alphafold/model/model.py:172: FutureWarning: jax.tree_map is deprecated, and will be removed in a future release. Use jax.tree_util.tree_map instead. [Compiling module jit_apply_fn.7] Very slow compile? If you want to file a bug, run with envvar XLA_FLAGS=--xla_dump_to=/tmp/foo and attach the results. Running model_3: 29%|██████████████████ | 2/7 [elapsed: 49:08 remaining: 2:02:28]2022-08-18 16:29:46.228967: E external/org_tensorflow/tensorflow/compiler/xla/service/slow_operation_alarm.cc:133] The operation took 6m40.557215143s [Compiling module jit_apply_fn.8] Very slow compile? If you want to file a bug, run with envvar XLA_FLAGS=--xla_dump_to=/tmp/foo and attach the results. Running model_4: 43%|██████████████████████████▏ | 3/7 [elapsed: 1:12:02 remaining: 1:35:05]2022-08-18 16:47:57.276966: E external/org_tensorflow/tensorflow/compiler/xla/service/slow_operation_alarm.cc:65] [Compiling module jit_apply_fn.9] Very slow compile? If you want to file a bug, run with envvar XLA_FLAGS=--xla_dump_to=/tmp/foo and attach the results. 2022-08-18 16:53:06.778986: E external/org_tensorflow/tensorflow/compiler/xla/service/slow_operation_alarm.cc:133] The operation took 7m9.502119733s [Compiling module jit_apply_fn.9] Very slow compile? If you want to file a bug, run with envvar XLA_FLAGS=--xla_dump_to=/tmp/foo and attach the results. Running model_5: 57%|██████████████████████████████████▊ | 4/7 [elapsed: 1:35:56 remaining: 1:11:28]2022-08-18 17:17:07.760154: E external/org_tensorflow/tensorflow/compiler/xla/service/slow_operation_alarm.cc:133] The operation took 7m11.676369326s [Compiling module jit_apply_fn.10] Very slow compile? If you want to file a bug, run with envvar XLA_FLAGS=--xla_dump_to=/tmp/foo and attach the results. Running model_2_ptm: 71%|██████████████████████████████████████████▏ | 5/7 [elapsed: 1:57:52 remaining: 46:16]2022-08-18 17:35:49.388007: E external/org_tensorflow/tensorflow/compiler/xla/service/slow_operation_alarm.cc:65] [Compiling module jit_apply_fn.11] Very slow compile? If you want to file a bug, run with envvar XLA_FLAGS=--xla_dump_to=/tmp/foo and attach the results. 2022-08-18 17:42:01.516711: E external/org_tensorflow/tensorflow/compiler/xla/service/slow_operation_alarm.cc:133] The operation took 8m12.12882662s [Compiling module jit_apply_fn.11] Very slow compile? If you want to file a bug, run with envvar XLA_FLAGS=--xla_dump_to=/tmp/foo and attach the results. Running model_2_ptm: 86%|██████████████████████████████████████████████████▌ | 6/7 [elapsed: 2:23:14 remaining: 23:53]Thu Aug 18 17:53:49 2022 WARNING |
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Could you please send me the sequence that caused a problem before? |
Hi I am running gget version: 0.3.7. When I run alphafold prediction I get this error:
gget alphafold AASEQUENCE
/home/ccadmin/anaconda3/envs/gget/lib/python3.9/site-packages/haiku/_src/data_structures.py:37: FutureWarning: jax.tree_structure is deprecated, and will be removed in a future release. Use jax.tree_util.tree_structure instead.
PyTreeDef = type(jax.tree_structure(None))
Fri Aug 12 20:12:30 2022 INFO Validating input sequence(s).
Using the single-chain model.
Fri Aug 12 20:12:30 2022 INFO Finding closest source for reference database.
Jackhmmer search: 5%|██▉ | 7/147 [elapsed: 11:32 remaining: 3:50:48]
Traceback (most recent call last):
File "/home/ccadmin/anaconda3/envs/gget/bin/gget", line 8, in
sys.exit(main())
File "/home/ccadmin/anaconda3/envs/gget/lib/python3.9/site-packages/gget/main.py", line 1439, in main
alphafold(
File "/home/ccadmin/anaconda3/envs/gget/lib/python3.9/site-packages/gget/gget_alphafold.py", line 467, in alphafold
raw_msa_results = get_msa(
File "/home/ccadmin/anaconda3/envs/gget/lib/python3.9/site-packages/gget/gget_alphafold.py", line 147, in get_msa
raw_msa_results[db_name].extend(jackhmmer_runner.query(fasta_path))
File "/home/ccadmin/anaconda3/envs/gget/lib/python3.9/site-packages/alphafold/data/tools/jackhmmer.py", line 205, in query
os.remove(db_local_chunk(i))
FileNotFoundError: [Errno 2] No such file or directory: '/home/ccadmin/tmp/jackhmmer/fcb45c67-8b27-4156-bbd8-9d11512babf2/uniref90_2021_03.fasta.8'
Any idea how to fix this?
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