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patrickbryant1 / SpeedPPI

Rapid protein-protein interaction network creation from multiple sequence alignments with Deep Learning
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SpeedPPI create_ppi_some_vs_some.sh issue #4

Closed RohanNathHERE closed 1 year ago

RohanNathHERE commented 1 year ago

Running pred 1 out of 1 Process Process-1: Traceback (most recent call last): File "/home/workspace2/anaconda3/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/workspace2/anaconda3/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/workspace2/SpeedPPI/src/tinyloader.py", line 39, in worker_fn output_queue.put((index, dataset[index])) File "/home/workspace2/SpeedPPI/./src/run_alphafold_some_vs_some.py", line 95, in getitem msa1, ox1 = pair_msas.read_a3m(self.msa_dir+self.target_id+'.a3m') File "/home/workspace2/SpeedPPI/src/alphafold/data/pair_msas.py", line 19, in read_a3m with open(infile, 'r') as file: FileNotFoundError: [Errno 2] No such file or directory: 'result//msas/CAB57340.1.a3m'

I'm getting the above error. What could be the issue?

This is my command: bash create_ppi_some_vs_some.sh /home/workspace2/psc3.pombe.fasta /home/workspace2/swi6.pombe.fasta /home/workspace2/hh-suite/build/bin/hhblits 0.5 result/

patrickbryant1 commented 1 year ago

Hi, This looks like the script can't find one of the MSAs. I think this may be related to the naming. Try to rename the ids to not have dots in the name. E.g. instead of CAB57340.1, do CAB57340_1.

RohanNathHERE commented 1 year ago

Yeah, that works perfectly, thanks!