I am running kneaddata and trimmomatic and get the following error. Any input would be appreciated.
Decontaminating …
Traceback (most recent call last):
File “/opt/miniconda3/bin/kneaddata”, line 33, in
sys.exit(load_entry_point(‘kneaddata==0.11.0’, ‘console_scripts’, ‘kneaddata’)())
File “/opt/miniconda3/lib/python3.9/site-packages/kneaddata/knead_data.py”, line 541, in main
final_output_files=run.decontaminate(args, full_path_output_prefix, trf_output_files)
File “/opt/miniconda3/lib/python3.9/site-packages/kneaddata/run.py”, line 561, in decontaminate
alignment_output_files = align([files_to_align[0][0],files_to_align[0][1]]+utilities.resolve_sublists(files_to_align[1:]),
File “/opt/miniconda3/lib/python3.9/site-packages/kneaddata/run.py”, line 164, in align
utilities.start_processes(commands,processors,verbose)
File “/opt/miniconda3/lib/python3.9/site-packages/kneaddata/utilities.py”, line 151, in start_processes
pool = multiprocessing.Pool(processes)
File “/opt/miniconda3/lib/python3.9/multiprocessing/context.py”, line 119, in Pool
return Pool(processes, initializer, initargs, maxtasksperchild,
File “/opt/miniconda3/lib/python3.9/multiprocessing/pool.py”, line 212, in init
self._repopulate_pool()
File “/opt/miniconda3/lib/python3.9/multiprocessing/pool.py”, line 303, in _repopulate_pool
return self._repopulate_pool_static(self._ctx, self.Process,
File “/opt/miniconda3/lib/python3.9/multiprocessing/pool.py”, line 326, in _repopulate_pool_static
w.start()
File “/opt/miniconda3/lib/python3.9/multiprocessing/process.py”, line 121, in start
self._popen = self._Popen(self)
File “/opt/miniconda3/lib/python3.9/multiprocessing/context.py”, line 284, in _Popen
return Popen(process_obj)
File “/opt/miniconda3/lib/python3.9/multiprocessing/popen_spawn_posix.py”, line 32, in init
super().init(process_obj)
File “/opt/miniconda3/lib/python3.9/multiprocessing/popen_fork.py”, line 19, in init
self._launch(process_obj)
File “/opt/miniconda3/lib/python3.9/multiprocessing/popen_spawn_posix.py”, line 42, in _launch
prep_data = spawn.get_preparation_data(process_obj._name)
File “/opt/miniconda3/lib/python3.9/multiprocessing/spawn.py”, line 176, in get_preparation_data
dir=os.getcwd(),
PermissionError: [Errno 1] Operation not permitted
Traceback (most recent call last):
File “”, line 1, in
File “”, line 1007, in _find_and_load
File “”, line 982, in _find_and_load_unlocked
File “”, line 925, in _find_spec
File “”, line 1414, in find_spec
File “”, line 1383, in _get_spec
File “”, line 1347, in _path_importer_cache
PermissionError: [Errno 1] Operation not permitted