/shared/vfvs_env/lib/python3.7/site-packages/boto3/compat.py:82: PythonDeprecationWarning: Boto3 will no longer support Python 3.7 starting December 13, 2023. To continue receiving service updates, bug fixes, and security updates please upgrade to Python 3.8 or later. More information can be found here: https://aws.amazon.com/blogs/developer/python-support-policy-updates-for-aws-sdks-and-tools/
  warnings.warn(warning, PythonDeprecationWarning)
ERROR:root:starting on localhost:56775
Error: Could not find or load main class com.martiansoftware.nailgun.NGServer
Caused by: java.lang.ClassNotFoundException: com.martiansoftware.nailgun.NGServer
multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "./vflp_run.py", line 1489, in run_obabel_general
    ret = subprocess.run(cmd, capture_output=True, text=True, timeout=timeout)
  File "/usr/lib64/python3.7/subprocess.py", line 490, in run
    stdout, stderr = process.communicate(input, timeout=timeout)
  File "/usr/lib64/python3.7/subprocess.py", line 964, in communicate
    stdout, stderr = self._communicate(input, endtime, timeout)
  File "/usr/lib64/python3.7/subprocess.py", line 1716, in _communicate
    self._check_timeout(endtime, orig_timeout, stdout, stderr)
  File "/usr/lib64/python3.7/subprocess.py", line 1011, in _check_timeout
    stderr=b''.join(stderr_seq) if stderr_seq else None)
subprocess.TimeoutExpired: Command '['obabel', '--gen3d', '-ismi', '/tmp/xgey42fp/obabel.conf.PV-009095522958_S0_T0_input.smi', '-opdb', '-O', '/tmp/xgey42fp/intermediate/AA/AAAA/0000/PV-009095522958/PV-009095522958_S0_T0/gen.pdb.tmp']' timed out after 15 seconds

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "./vflp_run.py", line 955, in run_conformation_generation
    run_conformation_instance(ctx, tautomer, ctx['config']['conformation_program_1'], output_file)
  File "./vflp_run.py", line 976, in run_conformation_instance
    raise error
  File "./vflp_run.py", line 973, in run_conformation_instance
    obabel_conformation(ctx, tautomer, output_file)
  File "./vflp_run.py", line 1881, in obabel_conformation
    obabel_generate_pdb_general(ctx, tautomer, output_file, conformation=1, must_have_output=0, timeout=ctx['config']['obabel_conformation_timeout'])
  File "./vflp_run.py", line 1833, in obabel_generate_pdb_general
    ret = run_obabel_general(cmd, timeout=timeout)
  File "./vflp_run.py", line 1491, in run_obabel_general
    raise RuntimeError(f"obabel timed out") from err
RuntimeError: obabel timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib64/python3.7/multiprocessing/pool.py", line 121, in worker
    result = (True, func(*args, **kwds))
  File "/usr/lib64/python3.7/multiprocessing/pool.py", line 44, in mapstar
    return list(map(*args))
  File "./vflp_run.py", line 188, in process_ligand
    process_stereoisomer(ctx, base_ligand, stereoisomer, completion_event['ligands'])
  File "./vflp_run.py", line 264, in process_stereoisomer
    process_tautomer(ctx, ligand, completion_ligands[tautomer_key])
  File "./vflp_run.py", line 534, in process_tautomer
    run_conformation_generation(ctx, tautomer, tautomer['pdb_file'])
  File "./vflp_run.py", line 957, in run_conformation_generation
    run_conformation_instance(ctx, tautomer, ctx['config']['conformation_program_2'], output_file)
  File "./vflp_run.py", line 971, in run_conformation_instance
    chemaxon_conformation(ctx, tautomer, output_file)
  File "./vflp_run.py", line 1405, in chemaxon_conformation
    molconvert_generate_conformation(ctx, tautomer, input_file, output_file_tmp)
  File "./vflp_run.py", line 1456, in molconvert_generate_conformation
    run_molconvert([ *(str(ctx['config']['molconvert_3D_options']).split()) ], input_file, output_file, ctx['config']['nailgun_port'], ctx['config']['nailgun_host'], timeout=ctx['config']['molconvert_conformation_timeout'])
  File "./vflp_run.py", line 1464, in run_molconvert
    run_chemaxon_general(local_args, nailgun_port, nailgun_host, must_have_output=0, timeout=timeout)
  File "./vflp_run.py", line 1135, in run_chemaxon_general
    ret = subprocess.run(cmd, capture_output=True, text=True, timeout=timeout)
  File "/usr/lib64/python3.7/subprocess.py", line 488, in run
    with Popen(*popenargs, **kwargs) as process:
  File "/usr/lib64/python3.7/subprocess.py", line 800, in __init__
    restore_signals, start_new_session)
  File "/usr/lib64/python3.7/subprocess.py", line 1551, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
OSError: [Errno 8] Exec format error: 'ng'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "./vflp_run.py", line 2695, in <module>
    main()
  File "./vflp_run.py", line 2685, in main
    process(ctx)
  File "./vflp_run.py", line 2341, in process
    process_collection(ctx, collection_key, collection, collection_data)
  File "./vflp_run.py", line 2381, in process_collection
    res = pool.map(process_ligand, tasklist)
  File "/usr/lib64/python3.7/multiprocessing/pool.py", line 268, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "/usr/lib64/python3.7/multiprocessing/pool.py", line 657, in get
    raise self._value
OSError: [Errno 8] Exec format error: 'ng'