I am new in python. I encountered an error when I used ribodetector.
The error was an the following:
ribodetector_cpu -t 20 `
-l 100
-i C:UserswinstDownloadsD0_2.cream.R1.001.fq.gz C:UserswinstDownloadsD0_2.cream.R2.001.fq.gz
-e rrna--chunk_size 100
-o C:UserswinstDownloadsD0reads.nonrrna.1.fq C:UserswinstDownloadsD0reads.nonrrna.2.fq
2024-04-24 00:07:24 : INFO Using high MCC model file: C:Userswinstanaconda3Libsite-packagesribodetectordata/ribodetector_600k_variable_len70_101_epoch47.onnx on CPU
2024-04-24 00:07:24 : INFO Classify reads with chunk size 100
2024-04-24 00:07:24 : INFO Writing output non-rRNA sequences into file: C:UserswinstDownloadsD0reads.nonrrna.1.fq, C:UserswinstDownloadsD0reads.nonrrna.2.fq
Traceback (most recent call last):
File “”, line 198, in _run_module_as_main
File “”, line 88, in run_code
File “C:Userswinstanaconda3Scriptsribodetector_cpu.exe_main.py”, line 7, in
File “C:Userswinstanaconda3Libsite-packagesribodetectordetect_cpu.py”, line 748, in main
seq_pred.detect()
File “C:Userswinstanaconda3Libsite-packagesribodetectordetect_cpu.py”, line 526, in detect
self.run_with_chunks()
File “C:Userswinstanaconda3Libsite-packagesribodetectordetect_cpu.py”, line 355, in run_with_chunks
p.start()
File “C:Userswinstanaconda3Libmultiprocessingprocess.py”, line 121, in start
self._popen = self._Popen(self)
^^^^^^^^^^^^^^^^^
File “C:Userswinstanaconda3Libmultiprocessingcontext.py”, line 224, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “C:Userswinstanaconda3Libmultiprocessingcontext.py”, line 336, in _Popen
return Popen(process_obj)
^^^^^^^^^^^^^^^^^^
File “C:Userswinstanaconda3Libmultiprocessingpopen_spawn_win32.py”, line 95, in init
reduction.dump(process_obj, to_child)
File “C:Userswinstanaconda3Libmultiprocessingreduction.py”, line 60, in dump
ForkingPickler(file, protocol).dump(obj)
TypeError: cannot pickle ‘onnxruntime.capi.onnxruntime_pybind11_state.InferenceSession’ object
Traceback (most recent call last):
File “”, line 1, in
File “C:Userswinstanaconda3Libmultiprocessingspawn.py”, line 122, in spawn_main
exitcode = _main(fd, parent_sentinel)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File “C:Userswinstanaconda3Libmultiprocessingspawn.py”, line 132, in _main
self = reduction.pickle.load(from_parent)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
EOFError: Ran out of input
Please help me to solve the error,
Thank you
I have tried to change the usage of CPU to 1, but it failed according to chatgpt’s suggestion.
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