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When hpo.txt is an empty file, the pipeline fails because phenoSim.R does not generate OMIM HPO file {{Job ID}}-dx, so main.py fails.
Log:
Feature engineering
input file: /out/jobid-vep-1.txt
type of input file: vepAnnotTab
outPrefix: /out/rami-test/r1
modules: curate,conserve
modules list: ['curate', 'conserve']
Traceback (most recent call last):
File "/run/annotation/main.py", line 486, in <module>
main()
File "/run/annotation/main.py", line 174, in main
omimHPOScoreDf = pd.read_csv(fileName, sep='\t')
File "/usr/local/lib/python3.8/dist-packages/pandas/util/_decorators.py", line 311, in wrapper
return func(*args, **kwargs)
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 680, in read_csv
return _read(filepath_or_buffer, kwds)
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 575, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 934, in __init__
self._engine = self._make_engine(f, self.engine)
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 1218, in _make_engine
self.handles = get_handle( # type: ignore[call-overload]
File "/usr/local/lib/python3.8/dist-packages/pandas/io/common.py", line 786, in get_handle
handle = open(
FileNotFoundError: [Errno 2] No such file or directory: '/out/jobid-dx'
The text was updated successfully, but these errors were encountered:
Previously, multiprocessing was utilized in the prediction step, resulting in increased memory consumption proportional
to the number of worker processes.
By refactoring the code to replace multiprocessing with a simple for loop, memory usage has been significantly reduced.
This change not only enhances efficiency by eliminating the overhead of virtual memory but also accelerates runtime performance.
When hpo.txt is an empty file, the pipeline fails because phenoSim.R does not generate OMIM HPO file {{Job ID}}-dx, so main.py fails.
Log:
The text was updated successfully, but these errors were encountered: