Closed brendaferrari closed 2 years ago
When I run the KlekotaRoth descriptor the run is not finishing, even though I get the results normally.
Interrupting the run I get this log:
KeyboardInterrupt --------------------------------------------------------------------------- KeyboardInterrupt Traceback (most recent call last) <ipython-input-5-fb2777cce1fe> in <module> 1 from functions.fingerprint_functions import KlekotaRoth 2 ----> 3 KlekotaRoth(mol_dir) c:\Users\Brenda\OneDrive\Documentos\Doutorado\QSAR\03.descriptor_preparation\functions\fingerprint_functions.py in KlekotaRoth(mol_dir) 322 fingerprint_descriptortypes = fp[fingerprint] 323 --> 324 padeldescriptor(mol_dir='dataset.smi', 325 d_file=fingerprint_output_file, 326 descriptortypes= fingerprint_descriptortypes, ~\AppData\Local\Programs\Python\Python38\lib\site-packages\padelpy\wrapper.py in padeldescriptor(maxruntime, waitingjobs, threads, d_2d, d_3d, config, convert3d, descriptortypes, detectaromaticity, mol_dir, d_file, fingerprints, log, maxcpdperfile, removesalt, retain3d, retainorder, standardizenitro, standardizetautomers, tautomerlist, usefilenameasmolname, sp_timeout, headless) 149 command += ' -usefilenameasmolname' 150 --> 151 _, err = _popen_timeout(command, sp_timeout) 152 if err != b'': 153 raise RuntimeError('PaDEL-Descriptor encountered an error: {}'.format( ~\AppData\Local\Programs\Python\Python38\lib\site-packages\padelpy\wrapper.py in _popen_timeout(command, timeout) 43 return (-1, b'PaDEL-Descriptor timed out during subprocess call') 44 else: ---> 45 return p.communicate() 46 47 ~\AppData\Local\Programs\Python\Python38\lib\subprocess.py in communicate(self, input, timeout) 1022 1023 try: -> 1024 stdout, stderr = self._communicate(input, endtime, timeout) 1025 except KeyboardInterrupt: 1026 # https://bugs.python.org/issue25942 ~\AppData\Local\Programs\Python\Python38\lib\subprocess.py in _communicate(self, input, endtime, orig_timeout) 1393 # calls communicate again. 1394 if self.stdout is not None: -> 1395 self.stdout_thread.join(self._remaining_time(endtime)) 1396 if self.stdout_thread.is_alive(): 1397 raise TimeoutExpired(self.args, orig_timeout) ~\AppData\Local\Programs\Python\Python38\lib\threading.py in join(self, timeout) 1009 1010 if timeout is None: -> 1011 self._wait_for_tstate_lock() 1012 else: 1013 # the behavior of a negative timeout isn't documented, but ~\AppData\Local\Programs\Python\Python38\lib\threading.py in _wait_for_tstate_lock(self, block, timeout) 1025 if lock is None: # already determined that the C code is done 1026 assert self._is_stopped -> 1027 elif lock.acquire(block, timeout): 1028 lock.release() 1029 self._stop() KeyboardInterrupt:
Thank you in advance.
Hi @brendaferrari,
Consider using the "maxruntime" argument in the "padeldescriptor" wrapper function (the argument is also available in the provided higher-level functions)!
Best, Travis
When I run the KlekotaRoth descriptor the run is not finishing, even though I get the results normally.
Interrupting the run I get this log:
Thank you in advance.