Alphafold 2.3.1+4 error while trying to build hexamer

[ProzacR]

Hi I tried to build hexamer from https://rest.uniprot.org/uniprotkb/P08050.fasta and got this error:

Organizing data and downloading params

Setup complete
/root/alphafold/run_alphafold.sh -d /root/ofs-alphafold-sym -o /root/outputs -t 2024-05-01 -f /sequence.fasta -m multimer_single -r all -c reduced_dbs
I0615 08:12:26.723825 139984488593216 templates.py:857] Using precomputed obsolete pdbs /root/ofs-alphafold-sym/pdb_mmcif/obsolete.dat.
I0615 08:12:29.160003 139984488593216 xla_bridge.py:353] Unable to initialize backend 'tpu_driver': NOT_FOUND: Unable to find driver in registry given worker:
I0615 08:12:29.324977 139984488593216 xla_bridge.py:353] Unable to initialize backend 'rocm': NOT_FOUND: Could not find registered platform with name: "rocm". Available platform names are: Host CUDA Interpreter
I0615 08:12:29.325304 139984488593216 xla_bridge.py:353] Unable to initialize backend 'tpu': module 'jaxlib.xla_extension' has no attribute 'get_tpu_client'
I0615 08:12:29.325401 139984488593216 xla_bridge.py:353] Unable to initialize backend 'plugin': xla_extension has no attributes named get_plugin_device_client. Compile TensorFlow with //tensorflow/compiler/xla/python:enable_plugin_device set to true (defaults to false) to enable this.
I0615 08:12:30.391323 139984488593216 run_alphafold.py:424] Have 5 models: ['model_1_multimer_v3_pred_0', 'model_1_multimer_v3_pred_1', 'model_1_multimer_v3_pred_2', 'model_1_multimer_v3_pred_3', 'model_1_multimer_v3_pred_4']
I0615 08:12:30.391481 139984488593216 run_alphafold.py:438] Using random seed 1358578226703238684 for the data pipeline
I0615 08:12:30.391683 139984488593216 run_alphafold.py:185] Predicting sequence
I0615 08:12:30.392326 139984488593216 pipeline_multimer.py:210] Running monomer pipeline on chain A: chain_1
I0615 08:12:30.393354 139977053050624 jackhmmer.py:133] Launching subprocess "/root/miniconda3/envs/alphafold/bin/jackhmmer -o /dev/null -A /tmp/tmphokxc8a4/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 32 -N 1 /tmp/tmpnyrhy62b.fasta /root/ofs-alphafold-sym/uniref90/uniref90.fasta"
I0615 08:12:30.416112 139977042560768 jackhmmer.py:133] Launching subprocess "/root/miniconda3/envs/alphafold/bin/jackhmmer -o /dev/null -A /tmp/tmpf3xbifr7/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 32 -N 1 /tmp/tmpnyrhy62b.fasta /root/ofs-alphafold-sym/mgnify/mgy_clusters_2022_05.fa"
I0615 08:12:30.433410 139982877382400 hhblits.py:128] Launching subprocess "/root/miniconda3/envs/alphafold/bin/hhblits -i /tmp/tmpnyrhy62b.fasta -cpu 32 -oa3m /tmp/tmpgnr77hlj/output.a3m -o /dev/null -n 3 -e 0.001 -maxseq 1000000 -realign_max 100000 -maxfilt 100000 -min_prefilter_hits 1000 -d /root/ofs-alphafold-sym/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt -d /root/ofs-alphafold-sym/uniref30/UniRef30_2021_03"
I0615 08:12:30.450512 139977053050624 utils.py:36] Started Jackhmmer (uniref90.fasta) query
I0615 08:12:30.456609 139977042560768 utils.py:36] Started Jackhmmer (mgy_clusters_2022_05.fa) query
I0615 08:12:30.473198 139982877382400 utils.py:36] Started HHblits query

I0615 08:25:51.010490 139982877382400 utils.py:40] Finished HHblits query in 800.537 seconds

I0615 08:27:52.732115 139977053050624 utils.py:40] Finished Jackhmmer (uniref90.fasta) query in 922.281 seconds

I0615 08:34:51.342365 139977042560768 utils.py:40] Finished Jackhmmer (mgy_clusters_2022_05.fa) query in 1340.886 seconds
I0615 08:34:53.173953 139984488593216 hmmbuild.py:121] Launching subprocess ['/root/miniconda3/envs/alphafold/bin/hmmbuild', '--hand', '--amino', '/tmp/tmpxf08jhpv/output.hmm', '/tmp/tmpxf08jhpv/query.msa']
I0615 08:34:53.219146 139984488593216 utils.py:36] Started hmmbuild query
I0615 08:34:53.848057 139984488593216 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/tmpxf08jhpv/query.msa
# output HMM file:                  /tmp/tmpxf08jhpv/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                 9053  2037   382     8.43  0.590


# CPU time: 0.61u 0.01s 00:00:00.62 Elapsed: 00:00:00.61




stderr:




I0615 08:34:53.848212 139984488593216 utils.py:40] Finished hmmbuild query in 0.629 seconds
I0615 08:34:53.850214 139984488593216 hmmsearch.py:103] Launching sub-process ['/root/miniconda3/envs/alphafold/bin/hmmsearch', '--noali', '--cpu', '32', '--F1', '0.1', '--F2', '0.1', '--F3', '0.1', '--incE', '100', '-E', '100', '--domE', '100', '--incdomE', '100', '-A', '/tmp/tmpifrv5_ff/output.sto', '/tmp/tmpifrv5_ff/query.hmm', '/root/ofs-alphafold-sym/pdb_seqres/pdb_seqres.txt']
I0615 08:34:53.893835 139984488593216 utils.py:36] Started hmmsearch (pdb_seqres.txt) query
I0615 08:34:57.047007 139984488593216 utils.py:40] Finished hmmsearch (pdb_seqres.txt) query in 3.153 seconds

I0615 08:34:58.751667 139984488593216 templates.py:940] Searching for template for: MGDWSALGKLLDKVQAYSTAGGKVWLSVLFIFRILLLGTAVESAWGDEQSAFRCNTQQPGCENVCYDKSFPISHVRFWVLQIIFVSVPTLLYLAHVFYVMRKEEKLNKKEEELKVAQTDGVNVEMHLKQIEIKKFKYGIEEHGKVKMRGGLLRTYIISILFKSVFEVAFLLIQWYIYGFSLSAVYTCKRDPCPHQVDCFLSRPTEKTIFIIFMLVVSLVSLALNIIELFYVFFKGVKDRVKGRSDPYHATTGPLSPSKDCGSPKYAYFNGCSSPTAPLSPMSPPGYKLVTGDRNNSSCRNYNKQASEQNWANYSAEQNRMGQAGSTISNSHAQPFDFPDDNQNAKKVAAGHELQPLAIVDQRPSSRASSRASSRPRPDDLEI
I0615 08:35:00.522959 139984488593216 templates.py:267] Found an exact template match 7f92_A.
I0615 08:35:00.533537 139984488593216 templates.py:267] Found an exact template match 7f92_B.
I0615 08:35:00.543685 139984488593216 templates.py:267] Found an exact template match 7f92_C.
I0615 08:35:00.553888 139984488593216 templates.py:267] Found an exact template match 7f92_D.
I0615 08:35:00.564073 139984488593216 templates.py:267] Found an exact template match 7f92_E.
I0615 08:35:00.574259 139984488593216 templates.py:267] Found an exact template match 7f92_F.
I0615 08:35:00.584450 139984488593216 templates.py:267] Found an exact template match 7f92_G.
I0615 08:35:00.594676 139984488593216 templates.py:267] Found an exact template match 7f92_H.
I0615 08:35:00.605183 139984488593216 templates.py:267] Found an exact template match 7f92_I.
I0615 08:35:00.615384 139984488593216 templates.py:267] Found an exact template match 7f92_J.
I0615 08:35:00.625580 139984488593216 templates.py:267] Found an exact template match 7f92_K.
I0615 08:35:00.635792 139984488593216 templates.py:267] Found an exact template match 7f92_L.
I0615 08:35:01.978062 139984488593216 templates.py:267] Found an exact template match 7f93_A.
I0615 08:35:01.988616 139984488593216 templates.py:267] Found an exact template match 7f93_B.
I0615 08:35:01.998881 139984488593216 templates.py:267] Found an exact template match 7f93_C.
I0615 08:35:02.009155 139984488593216 templates.py:267] Found an exact template match 7f93_D.
I0615 08:35:02.019567 139984488593216 templates.py:267] Found an exact template match 7f93_E.
I0615 08:35:02.029883 139984488593216 templates.py:267] Found an exact template match 7f93_F.
I0615 08:35:02.040257 139984488593216 templates.py:267] Found an exact template match 7f93_G.
I0615 08:35:02.050508 139984488593216 templates.py:267] Found an exact template match 7f93_H.
I0615 08:35:02.060756 139984488593216 templates.py:267] Found an exact template match 7f93_I.
I0615 08:35:02.071066 139984488593216 templates.py:267] Found an exact template match 7f93_J.
I0615 08:35:02.081320 139984488593216 templates.py:267] Found an exact template match 7f93_K.
I0615 08:35:02.091693 139984488593216 templates.py:267] Found an exact template match 7f93_L.
I0615 08:35:03.530795 139984488593216 templates.py:267] Found an exact template match 7xq9_A.
I0615 08:35:03.541381 139984488593216 templates.py:267] Found an exact template match 7xq9_B.
I0615 08:35:03.551830 139984488593216 templates.py:267] Found an exact template match 7xq9_C.
I0615 08:35:03.562224 139984488593216 templates.py:267] Found an exact template match 7xq9_D.
I0615 08:35:03.572590 139984488593216 templates.py:267] Found an exact template match 7xq9_E.
I0615 08:35:03.583369 139984488593216 templates.py:267] Found an exact template match 7xq9_F.
I0615 08:35:03.593803 139984488593216 templates.py:267] Found an exact template match 7xq9_G.
I0615 08:35:03.604223 139984488593216 templates.py:267] Found an exact template match 7xq9_H.
I0615 08:35:03.614635 139984488593216 templates.py:267] Found an exact template match 7xq9_I.
I0615 08:35:03.625073 139984488593216 templates.py:267] Found an exact template match 7xq9_J.
I0615 08:35:03.635517 139984488593216 templates.py:267] Found an exact template match 7xq9_K.
I0615 08:35:03.645902 139984488593216 templates.py:267] Found an exact template match 7xq9_L.
I0615 08:35:06.450583 139984488593216 templates.py:267] Found an exact template match 7xqb_A.
I0615 08:35:06.464332 139984488593216 templates.py:267] Found an exact template match 7xqb_B.
I0615 08:35:06.477809 139984488593216 templates.py:267] Found an exact template match 7xqb_C.
I0615 08:35:06.491731 139984488593216 templates.py:267] Found an exact template match 7xqb_D.
I0615 08:35:06.505325 139984488593216 templates.py:267] Found an exact template match 7xqb_E.
I0615 08:35:06.518888 139984488593216 templates.py:267] Found an exact template match 7xqb_F.
I0615 08:35:06.532431 139984488593216 templates.py:267] Found an exact template match 7xqb_G.
I0615 08:35:06.545999 139984488593216 templates.py:267] Found an exact template match 7xqb_H.
I0615 08:35:06.559555 139984488593216 templates.py:267] Found an exact template match 7xqb_I.
I0615 08:35:06.573681 139984488593216 templates.py:267] Found an exact template match 7xqb_J.
I0615 08:35:06.587275 139984488593216 templates.py:267] Found an exact template match 7xqb_K.
I0615 08:35:06.600867 139984488593216 templates.py:267] Found an exact template match 7xqb_L.
Traceback (most recent call last):
File "/root/alphafold/run_alphafold.py", line 468, in <module>
app.run(main)
File "/root/miniconda3/envs/alphafold/lib/python3.9/site-packages/absl/app.py", line 312, in run
_run_main(main, args)
File "/root/miniconda3/envs/alphafold/lib/python3.9/site-packages/absl/app.py", line 258, in _run_main
sys.exit(main(argv))
File "/root/alphafold/run_alphafold.py", line 443, in main
predict_structure(
File "/root/alphafold/run_alphafold.py", line 196, in predict_structure
feature_dict = data_pipeline.process(
File "/root/alphafold/alphafold/data/pipeline_multimer.py", line 264, in process
chain_features = self._process_single_chain(
File "/root/alphafold/alphafold/data/pipeline_multimer.py", line 212, in _process_single_chain
chain_features = self._monomer_data_pipeline.process(
File "/root/alphafold/alphafold/data/pipeline.py", line 249, in process
templates_result = self.template_featurizer.get_templates(
File "/root/alphafold/alphafold/data/templates.py", line 960, in get_templates
result = _process_single_hit(
File "/root/alphafold/alphafold/data/templates.py", line 737, in _process_single_hit
cif_string = _read_file(cif_path)
File "/root/alphafold/alphafold/data/templates.py", line 681, in _read_file
with open(path, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/root/ofs-alphafold-sym/pdb_mmcif/mmcif_files/7z1t.cif'

====================
2023-06-15 08:35:08,014 flytekit ERROR Exception occured when executing task: alphafold failed with exit code 1
====================
Traceback (most recent call last):
  File "/root/miniconda3/envs/alphafold/lib/python3.9/site-packages/flytekit/exceptions/scopes.py", line 204, in user_entry_point
    return wrapped(*args, **kwargs)
  File "/root/wf/__init__.py", line 382, in alphafold
    raise Exception(f"alphafold failed with exit code {retval}")
Exception: alphafold failed with exit code 1


During handling of the above exception, another exception occurred:


Traceback (most recent call last):
  File "/root/miniconda3/envs/alphafold/lib/python3.9/site-packages/flytekit/core/base_task.py", line 478, in dispatch_execute
    native_outputs = self.execute(**native_inputs)
  File "/root/miniconda3/envs/alphafold/lib/python3.9/site-packages/flytekit/core/python_function_task.py", line 200, in execute
    return exception_scopes.user_entry_point(self._task_function)(**kwargs)
  File "/root/miniconda3/envs/alphafold/lib/python3.9/site-packages/flytekit/exceptions/scopes.py", line 215, in user_entry_point
    raise FlyteScopedUserException(*_exc_info())
flytekit.exceptions.scopes.FlyteScopedUserException: alphafold failed with exit code 1
====================
2023-06-15 08:35:08,015 flytekit.entrypoint ERROR 
!! Begin User Error Captured by Flyte !!
Traceback (most recent call last):


      File "/root/miniconda3/envs/alphafold/lib/python3.9/site-packages/flytekit/exceptions/scopes.py", line 204, in user_entry_point
        return wrapped(*args, **kwargs)
      File "/root/wf/__init__.py", line 382, in alphafold
        raise Exception(f"alphafold failed with exit code {retval}")


Message:


    alphafold failed with exit code 1


User error.
!! End Error Captured by Flyte !!


====================

From the literature, it is known that it should be hexamer. I believe the issue continues with other high-similarity sequences forming hexamers from other organisms or the same organism. Any idea what could be wrong?