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labsyspharm / quantification

Quantification module for mcmicro
https://github.com/labsyspharm/mcmicro
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Error on o2 #9

Closed DenisSch closed 4 years ago

DenisSch commented 4 years ago

I get following error on o2. I will updated the yaml and check again.

Extracting sinle-cell data for /n/scratch2/ds230/MouseModelData/H1_775/$...
Traceback (most recent call last):
  File "/n/groups/lsp/mcmicro/quantification/CommandSingleCellExtraction.py", line 11, in <module>
    SingleCellDataExtraction.MultiExtractSingleCells(**args)
  File "/n/groups/lsp/mcmicro/quantification/SingleCellDataExtraction.py", line 181, in MultiExtractSingleCells
    ExtractSingleCells(mask,image,channel_names,output)
  File "/n/groups/lsp/mcmicro/quantification/SingleCellDataExtraction.py", line 164, in ExtractSingleCells
    output = Path(output)
  File "/home/ds230/.conda/envs/quantification/lib/python3.8/pathlib.py", line 1033, in __new__
    self = cls._from_parts(args, init=False)
  File "/home/ds230/.conda/envs/quantification/lib/python3.8/pathlib.py", line 674, in _from_parts
    drv, root, parts = self._parse_args(args)
  File "/home/ds230/.conda/envs/quantification/lib/python3.8/pathlib.py", line 658, in _parse_args
    a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not NoneType