text: user5180: I am running DMPfold, "seq2maps.sh" ran successfully, but whrn running "run_dmpfold.sh", it gives me this error:
     Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
  Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
  seed =  30603
  Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
  /media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/run_dmpfold.sh: line 177: c600m2-tail-before-lysin-sequence_[1-9]*.pdb: No such file or directory
  No atoms read from PDB file
  0 models read from PDB file
  Outliers:
  
  
  Traceback (most recent call last):
    File "/media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/nn/dmp-softmax/pytorch_dmp_iterdistpred_cb.py", line 82, in <module>
      main()
    File "/media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/nn/dmp-softmax/pytorch_dmp_iterdistpred_cb.py", line 55, in main
      with open(sys.argv[3], 'r') as refpdbfile:
  FileNotFoundError: [Errno 2] No such file or directory: 'best_qdope.pdb'
  Traceback (most recent call last):
    File "/media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/nn/dmp-hb/pytorch_iterdmp_hbpred.py", line 75, in <module>
      main()
    File "/media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/nn/dmp-hb/pytorch_iterdmp_hbpred.py", line 53, in main
      with open(sys.argv[3], 'r') as refpdbfile:
  FileNotFoundError: [Errno 2] No such file or directory: 'best_qdope.pdb'
  No valid current contacts.
  
  Can you please let me know how this can be solved? 
  the comand line is:
  run_dmpfold.sh sequence.fasta sequence.21c sequence.map ./dmpfold-lysin 10 500 &> dmpfold-log.log
  
  Thanks!
  
  user4622: The target variable, which is set to the first part of the sequence file name, should be sequence according to your given command line. However the error message thinks it is c600m2-tail-before-lysin-sequence. Have you edited the command line for simplicity?
  I'm a little worried about the floating point errors, which are almost certainly from CNS as there are 3 CNS calls and the error shows up 3 times. I would test your CNS installation to see if everything is okay - maybe try some examples from their website. An error there would explain why no output is generated.
  You can ignore any errors below line 5 of the above program output for now, as they are follow-on errors. In particular the question title isn't the 'real' error here, the real error is that no PDB files are generated on line 160.
  By the way, I wouldn't use 10 500 as parameters for iteration number and number of models. It will take ages to run. I'd just use the defaults (omit the arguments), which we find gives good results.
  Finally, I'll point out that the DMPfold repository has an issue tracker where you can raise any future issues. Though we may as well finish debugging this one here since we've started!
  
original_text: 5180: <p>I am running DMPfold, "seq2maps.sh" ran successfully, but whrn running "run_dmpfold.sh", it gives me this error:</p>
  
  <pre><code>   Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
  Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
  seed =  30603
  Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
  /media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/run_dmpfold.sh: line 177: c600m2-tail-before-lysin-sequence_[1-9]*.pdb: No such file or directory
  No atoms read from PDB file
  0 models read from PDB file
  Outliers:
  
  
  Traceback (most recent call last):
    File "/media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/nn/dmp-softmax/pytorch_dmp_iterdistpred_cb.py", line 82, in &lt;module&gt;
      main()
    File "/media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/nn/dmp-softmax/pytorch_dmp_iterdistpred_cb.py", line 55, in main
      with open(sys.argv[3], 'r') as refpdbfile:
  FileNotFoundError: [Errno 2] No such file or directory: 'best_qdope.pdb'
  Traceback (most recent call last):
    File "/media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/nn/dmp-hb/pytorch_iterdmp_hbpred.py", line 75, in &lt;module&gt;
      main()
    File "/media/Deepak/NPRP10/softwares/dmpfold/DMPfold-master/nn/dmp-hb/pytorch_iterdmp_hbpred.py", line 53, in main
      with open(sys.argv[3], 'r') as refpdbfile:
  FileNotFoundError: [Errno 2] No such file or directory: 'best_qdope.pdb'
  No valid current contacts.
  </code></pre>
  
  <p>Can you please let me know how this can be solved? </p>
  
  <p>the comand line is:</p>
  
  <pre><code>run_dmpfold.sh sequence.fasta sequence.21c sequence.map ./dmpfold-lysin 10 500 &amp;&gt; dmpfold-log.log
  </code></pre>
  
  <p>Thanks!</p>
   4622: <p>The <code>target</code> variable, which is set to the first part of the sequence file name, should be <code>sequence</code> according to your given command line. However the error message thinks it is <code>c600m2-tail-before-lysin-sequence</code>. Have you edited the command line for simplicity?</p>
  
  <p>I'm a little worried about the floating point errors, which are almost certainly from CNS as there are 3 CNS calls and the error shows up 3 times. I would test your CNS installation to see if everything is okay - maybe try some examples from <a href="https://www.mrc-lmb.cam.ac.uk/public/xtal/doc/cns/cns_1.3/getting_started/frame.html" rel="nofollow noreferrer">their website</a>. An error there would explain why no output is generated.</p>
  
  <p>You can ignore any errors below line 5 of the above program output for now, as they are follow-on errors. In particular the question title isn't the 'real' error here, the real error is that no PDB files are generated on <a href="https://github.com/psipred/DMPfold/blob/master/run_dmpfold.sh#L160" rel="nofollow noreferrer">line 160</a>.</p>
  
  <p>By the way, I wouldn't use <code>10 500</code> as parameters for iteration number and number of models. It will take ages to run. I'd just use the defaults (omit the arguments), which we find gives good results.</p>
  
  <p>Finally, I'll point out that the <a href="https://github.com/psipred/DMPfold" rel="nofollow noreferrer">DMPfold repository</a> has an issue tracker where you can raise any future issues. Though we may as well finish debugging this one here since we've started!</p>
  