Closed balwierz closed 8 years ago
I tested it with 1 cpu only (and one chromosome) and I am getting now the following error:
Traceback (most recent call last):
File "/usr/local/bin/epic", line 165, in <module>
run_epic(args)
File "/usr/local/lib/python2.7/dist-packages/epic/run/run_epic.py", line 42, in run_epic
args.number_cores)
File "/usr/local/lib/python2.7/dist-packages/epic/utils/helper_functions.py", line 37, in merge_chip_and_input
for chip_df, input_df in zip(chip_dfs, input_dfs))
File "/usr/local/lib/python2.7/dist-packages/joblib/parallel.py", line 754, in __call__
while self.dispatch_one_batch(iterator):
File "/usr/local/lib/python2.7/dist-packages/joblib/parallel.py", line 604, in dispatch_one_batch
self._dispatch(tasks)
File "/usr/local/lib/python2.7/dist-packages/joblib/parallel.py", line 567, in _dispatch
job = self._backend.apply_async(batch, callback=cb)
File "/usr/local/lib/python2.7/dist-packages/joblib/_parallel_backends.py", line 109, in apply_async
result = ImmediateResult(func)
File "/usr/local/lib/python2.7/dist-packages/joblib/_parallel_backends.py", line 322, in __init__
self.results = batch()
File "/usr/local/lib/python2.7/dist-packages/joblib/parallel.py", line 127, in __call__
return [func(*args, **kwargs) for func, args, kwargs in self.items]
File "/usr/local/lib/python2.7/dist-packages/epic/utils/helper_functions.py", line 24, in _merge_chip_and_input
assert len(merged_df) == chip_df_nb_bins
AssertionError
I suspect the first error is some strange error in pandas and joblib - or an interaction between them - which I have experienced myself. Could you please
1) report the current version numbers of those two libraries 2) try upgrading them, reporting success/fail and new version numbers?
Thanks. Will start looking at the AssertionError
.
Moving the new question to #31
python-pandas 0.18.1 python3-pandas 0.18.1 python-joblib 0.9.4 python3-joblib 0.9.4 (all latest in Debian Stretch)
Update: a new joblib
(0.10.0) is installed by pip
to python2.7/dist-packages
Unfortunately I need to report another problem: