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
hhlib=/home/sliu/Tools/DeepFold_suite/distance/DeepPotential_04132020/bin/hhsuite2/bin/..
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
Done
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>
prepare_longdistance(alnfile,savefile)
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
typed_storage._storage._set_from_file(
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.