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Error During Computing Consensus Step #235
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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. |
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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.
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.
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