Error During Computing Consensus Step

[rybioinf]

Dear Flye Developers,

I am running into an issue during the computing concencus step. I am working with a prokaryote genome ~5m bp with relatively poor data (ONT run with quality score cutoff of 9, ~12x coverage, plenty of reads 2-5kb). This runs as follows.

[2021-12-09 13:43:32] INFO: >>>STAGE: consensus
[2021-12-09 13:43:32] INFO: Running Minimap2
[2021-12-09 13:43:42] INFO: Computing consensus
Traceback (most recent call last):
File "", line 1, in
File "/Users/ryan/miniconda3/lib/python3.9/multiprocessing/spawn.py", line 116, in spawn_main
exitcode = _main(fd, parent_sentinel)
File "/Users/ryan/miniconda3/lib/python3.9/multiprocessing/spawn.py", line 125, in _main
prepare(preparation_data)
File "/Users/ryan/miniconda3/lib/python3.9/multiprocessing/spawn.py", line 236, in prepare
_fixup_main_from_path(data['init_main_from_path'])
File "/Users/ryan/miniconda3/lib/python3.9/multiprocessing/spawn.py", line 287, in _fixup_main_from_path
main_content = runpy.run_path(main_path,
File "/Users/ryan/miniconda3/lib/python3.9/runpy.py", line 268, in run_path
return _run_module_code(code, init_globals, run_name,
File "/Users/ryan/miniconda3/lib/python3.9/runpy.py", line 97, in _run_module_code
_run_code(code, mod_globals, init_globals,
File "/Users/ryan/miniconda3/lib/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/Users/ryan/documents/Flye_Assembly/Flye/bin/flye", line 25, in
sys.exit(main())
File "/Users/ryan/documents/Flye_Assembly/Flye/flye/main.py", line 830, in main
_run(args)
File "/Users/ryan/documents/Flye_Assembly/Flye/flye/main.py", line 583, in _run
jobs[i].run()
File "/Users/ryan/documents/Flye_Assembly/Flye/flye/main.py", line 322, in run
consensus_fasta = cons.get_consensus(out_alignment, self.in_contigs,
File "/Users/ryan/documents/Flye_Assembly/Flye/flye/polishing/consensus.py", line 71, in get_consensus
aln_reader = SynchronizedSamReader(alignment_path, contigs_fasta,
File "/Users/ryan/documents/Flye_Assembly/Flye/flye/utils/sam_parser.py", line 199, in init
self.shared_manager = multiprocessing.Manager()
File "/Users/ryan/miniconda3/lib/python3.9/multiprocessing/context.py", line 57, in Manager
m.start()
File "/Users/ryan/miniconda3/lib/python3.9/multiprocessing/managers.py", line 553, in start
self._process.start()
File "/Users/ryan/miniconda3/lib/python3.9/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/Users/ryan/miniconda3/lib/python3.9/multiprocessing/context.py", line 284, in _Popen
return Popen(process_obj)
File "/Users/ryan/miniconda3/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 32, in init
super().init(process_obj)
File "/Users/ryan/miniconda3/lib/python3.9/multiprocessing/popen_fork.py", line 19, in init
self._launch(process_obj)
File "/Users/ryan/miniconda3/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 42, in _launch
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/ryan/miniconda3/lib/python3.9/multiprocessing/spawn.py", line 154, in get_preparation_data
_check_not_importing_main()
File "/Users/ryan/miniconda3/lib/python3.9/multiprocessing/spawn.py", line 134, in _check_not_importing_main
raise RuntimeError('''
RuntimeError:
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.

    This probably means that you are not using fork to start your
    child processes and you have forgotten to use the proper idiom
    in the main module:

        if __name__ == '__main__':
            freeze_support()
            ...

    The "freeze_support()" line can be omitted if the program
    is not going to be frozen to produce an executable.

Traceback (most recent call last):
File "/Users/ryan/documents/Flye_Assembly/Flye/bin/flye", line 25, in
sys.exit(main())
File "/Users/ryan/documents/Flye_Assembly/Flye/flye/main.py", line 830, in main
_run(args)
File "/Users/ryan/documents/Flye_Assembly/Flye/flye/main.py", line 583, in _run
jobs[i].run()
File "/Users/ryan/documents/Flye_Assembly/Flye/flye/main.py", line 322, in run
consensus_fasta = cons.get_consensus(out_alignment, self.in_contigs,
File "/Users/ryan/documents/Flye_Assembly/Flye/flye/polishing/consensus.py", line 71, in get_consensus
aln_reader = SynchronizedSamReader(alignment_path, contigs_fasta,
File "/Users/ryan/documents/Flye_Assembly/Flye/flye/utils/sam_parser.py", line 199, in init
self.shared_manager = multiprocessing.Manager()
File "/Users/ryan/miniconda3/lib/python3.9/multiprocessing/context.py", line 57, in Manager
m.start()
File "/Users/ryan/miniconda3/lib/python3.9/multiprocessing/managers.py", line 557, in start
self._address = reader.recv()
File "/Users/ryan/miniconda3/lib/python3.9/multiprocessing/connection.py", line 255, in recv
buf = self._recv_bytes()
File "/Users/ryan/miniconda3/lib/python3.9/multiprocessing/connection.py", line 419, in _recv_bytes
buf = self._recv(4)
File "/Users/ryan/miniconda3/lib/python3.9/multiprocessing/connection.py", line 388, in _recv
raise EOFError
EOFError

flye.log

Any advice would be much appreciated.

[rybioinf]

I have also tried running Flye with data from a much better run from the same organism (~420x coverage) with the --asm-coverage 100 extension. I still ran into the same error at the same part of the job.