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weird random error No such file or directory: 'temp.pdb' and -temperature: command not found #89

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18217265596 opened this issue Aug 1, 2024 · 0 comments

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@18217265596
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mpnn_fr could run some time ,did produce sequences ( i chose to produce structure also)
and randomly produce this error and stop:

and re-run would also be fine and no err
idk what triggers it
temp.pdb is not one of my pdb names
and in the error it cant recognize temperature

idk if its something wrong with the slurm system or sth else
but im using hpc so i assume its not problem of slurm

Traceback (most recent call last):
File "dl_interface_design.py", line 427, in
if args.debug: proteinmpnn_runner.run_model(pdb, args)
File "dl_interface_design.py", line 294, in run_model
self.proteinmpnn_fastrelax(sample_feats)
File "dl_interface_design.py", line 267, in proteinmpnn_fastrelax
seqs_scores = self.sequence_optimize(sample_feats)
File "/dl_interface_design.py", line 196, in sequence_optimize
feature_dict = mpnn_util.generate_seqopt_features(pdbfile, sample_feats.chains)
File "/dssg/home/acct-clswg/clswg/apps/dl_binder_new/dl_binder_design/mpnn_fr/util_protein_mpnn.py", line 174, in generate_seqopt_features
xyz, seq = parse_PDB_biounits(pdbfile, atoms=['N','CA','C','O'], chain=letter)
File "/dssg/home/acct-clswg/clswg/apps/dl_binder_new/dl_binder_design/mpnn_fr/util_protein_mpnn.py", line 50, in parse_PDB_biounits
for line in open(x,"rb"):
FileNotFoundError: [Errno 2] No such file or directory: 'temp.pdb'
/tmp/slurmd/job35750471/slurm_script: line 21: -temperature: command not found

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