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fatchord / WaveRNN

WaveRNN Vocoder + TTS
https://fatchord.github.io/model_outputs/
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Error During Computing Consensus Step #235

Open rybioinf opened 2 years ago

rybioinf commented 2 years ago

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 commented 2 years ago

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.