unexpected EOF in DeepMSA

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Moderator: robpearc

Posts: 4
Joined: Thu Jan 12, 2023 12:15 pm

unexpected EOF in DeepMSA

Post by SLarmadillo »

The following process was automatically exiting and starting over continuously for three days after displaying RuntimeError: unexpected EOF, expected 408096 more bytes. The file might be corrupted. Is this a normal process, or will I never get a result with this Error, and will the process repeat forever?

Code: Select all

starting time: Thu 19 Jan 13:33:37 CET 2023
pwd /home/sliu/Tools/DeepFold_suite
warning: protein.a3m does not exist! use protein.aln instead
---- run DeepPotential ----
cuda is ready? : True
DeepPotential.a3m is in A2M, A3M or FASTA format
Read DeepPotential.a3m with 40323 sequences
Alignment in DeepPotential.a3m contains 310 match states
671 out of 40323 sequences passed filter (up to 21% position-dependent max pairwise sequence identity)
Effective number of sequences exp(entropy) = 12.2
WARNING: MSA temp looks too diverse (Neff=12.2>11). Better check it with an alignment viewer for non-homologous segments. Also consider building the MSA with hhblits using the - option to limit MSA diversity.
Writing HMM to DeepPotential.hmm
predicting 7
predicting 10
predicting 11
predicting 15
predicting 20
predicting 22
predicting 23
predicting 24
predicting 25
predicting 28
predicting 29
Traceback (most recent call last):
  File "/home/sliu/Tools/DeepFold_suite/distance/DeepPotential_04132020/predict.py", line 234, in <module>
  File "/home/sliu/Tools/DeepFold_suite/distance/DeepPotential_04132020/predict.py", line 139, in prepare_longdistance
    model_dict=torch.load(os.path.join(model_dirs,model_file), map_location=lambda storage, loc: storage)
  File "/home/sliu/.local/lib/python3.10/site-packages/torch/serialization.py", line 795, in load
    return _legacy_load(opened_file, map_location, pickle_module, **pickle_load_args)
  File "/home/sliu/.local/lib/python3.10/site-packages/torch/serialization.py", line 1020, in _legacy_load
RuntimeError: unexpected EOF, expected 408096 more bytes. The file might be corrupted.
ending time: Thu 19 Jan 14:46:52 CET 2023
/home/sliu/Tools/DeepFold_suite/QAQRtest/MSA/protein.aln is available. Let's predict spatial restraints.
Posts: 145
Joined: Tue May 04, 2021 5:04 pm

Re: unexpected EOF in DeepMSA

Post by jlspzw »

Dear user,

We have contacted the author of DeepFold, and all the related issues, you can report to him if you don't get feedback from him here.
His email address is robpearc@umich.edu .

Thank you.

IT Team
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