segment command errors out with #1004
Description
I am using the docker image cnvkit:0.9.13 updated according to #1003
Running the command:
cnvkit.py segment \
--output ${SAMPLE}.baf.cns \
--method cbs --min-variant-depth 10 \
--processes 8 --sample-id ${SAMPLE} \
--smooth-cbs \
--vcf ${SAMPLE}.HC.vcf.gz \
${SAMPLE}EA27-1091525.cnr
Results in the error:
concurrent.futures.process._RemoteTraceback:
"""
Traceback (most recent call last):
File "/opt/conda/lib/python3.13/concurrent/futures/process.py", line 254, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "/opt/conda/lib/python3.13/concurrent/futures/process.py", line 203, in _process_chunk
return [fn(*args) for args in chunk]
~~^^^^^^^
File "/opt/conda/lib/python3.13/site-packages/cnvlib/segmentation/__init__.py", line 185, in _ds
return _do_segmentation(*args)
File "/opt/conda/lib/python3.13/site-packages/cnvlib/segmentation/__init__.py", line 293, in _do_segmentation
hmm.variants_in_segment(subvarr, segment)
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.13/site-packages/cnvlib/segmentation/hmm.py", line 401, in variants_in_segment
X_3d = observations.reshape(1, -1, 1).astype(np.float32)
^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.13/site-packages/pandas/core/generic.py", line 6206, in __getattr__
return object.__getattribute__(self, name)
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^
AttributeError: 'Series' object has no attribute 'reshape'. Did you mean: 'shape'?
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/opt/conda/bin/cnvkit.py", line 7, in <module>
sys.exit(main())
~~~~^^
File "/opt/conda/lib/python3.13/site-packages/cnvlib/cnvkit.py", line 11, in main
args.func(args)
~~~~~~~~~^^^^^^
File "/opt/conda/lib/python3.13/site-packages/cnvlib/commands.py", line 1067, in _cmd_segment
results = segmentation.do_segmentation(
cnarr,
...<9 lines>...
smooth_cbs=args.smooth_cbs,
)
File "/opt/conda/lib/python3.13/site-packages/cnvlib/segmentation/__init__.py", line 137, in do_segmentation
rets = list(
pool.map(
...<17 lines>...
)
)
File "/opt/conda/lib/python3.13/concurrent/futures/process.py", line 617, in _chain_from_iterable_of_lists
for element in iterable:
^^^^^^^^
File "/opt/conda/lib/python3.13/concurrent/futures/_base.py", line 619, in result_iterator
yield _result_or_cancel(fs.pop())
~~~~~~~~~~~~~~~~~^^^^^^^^^^
File "/opt/conda/lib/python3.13/concurrent/futures/_base.py", line 317, in _result_or_cancel
return fut.result(timeout)
~~~~~~~~~~^^^^^^^^^
File "/opt/conda/lib/python3.13/concurrent/futures/_base.py", line 456, in result
return self.__get_result()
~~~~~~~~~~~~~~~~~^^
File "/opt/conda/lib/python3.13/concurrent/futures/_base.py", line 401, in __get_result
raise self._exception
AttributeError: 'Series' object has no attribute 'reshape'