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Can't pickle the function mf.parts.bam_writer #131

@falsetry1514

Description

@falsetry1514

It occurs in the job tag_reads_bc_umi, maybe in multiprocess env it can't be pickled well.
Could you tell me how to fix this bug.

Traceback (most recent call last):
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/site-packages/spacemake/bin/fastq_to_uBAM.py", line 409, in
res = cmdline()
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/site-packages/spacemake/bin/fastq_to_uBAM.py", line 405, in cmdline
return main(args)
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/site-packages/spacemake/bin/fastq_to_uBAM.py", line 257, in main
return w.run()
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/site-packages/mrfifo/init.py", line 209, in run
job.start()
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/site-packages/mrfifo/init.py", line 43, in start
self.p.start()
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/multiprocessing/context.py", line 224, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/multiprocessing/context.py", line 288, in _Popen
return Popen(process_obj)
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/multiprocessing/popen_spawn_posix.py", line 32, in init
super().init(process_obj)
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/multiprocessing/popen_fork.py", line 19, in init
self._launch(process_obj)
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/multiprocessing/popen_spawn_posix.py", line 47, in _launch
reduction.dump(process_obj, fp)
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/multiprocessing/reduction.py", line 60, in dump
ForkingPickler(file, protocol).dump(obj)
_pickle.PicklingError: Can't pickle <function bam_writer at 0x1387a68c0>: it's not the same object as mrfifo.parts.bam_writer
Traceback (most recent call last):
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/site-packages/spacemake/bin/fastq_to_uBAM.py", line 409, in
res = cmdline()
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/site-packages/spacemake/bin/fastq_to_uBAM.py", line 405, in cmdline
return main(args)
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/site-packages/spacemake/bin/fastq_to_uBAM.py", line 257, in main
return w.run()
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/site-packages/mrfifo/init.py", line 209, in run
job.start()
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/site-packages/mrfifo/init.py", line 43, in start
self.p.start()
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/multiprocessing/context.py", line 224, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/multiprocessing/context.py", line 288, in _Popen
return Popen(process_obj)
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/multiprocessing/popen_spawn_posix.py", line 32, in init
super().init(process_obj)
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/multiprocessing/popen_fork.py", line 19, in init
self._launch(process_obj)
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/multiprocessing/popen_spawn_posix.py", line 47, in _launch
reduction.dump(process_obj, fp)
File "/Users/server3/miniforge3/envs/spacemake/lib/python3.10/multiprocessing/reduction.py", line 60, in dump
ForkingPickler(file, protocol).dump(obj)
_pickle.PicklingError: Can't pickle <function bam_writer at 0x13a59e8c0>: it's not the same object as mrfifo.parts.bam_writer

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