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epigen / scifiRNA-seq

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KeyError: 'species_mixing' #11

Open Jssmith91 opened 3 years ago

Jssmith91 commented 3 years ago

Hi

I am trying to run a test analysis using the file PD212_scifi_1N_4lines_7650_nuclei.bam from the publication data.

Perhaps i am misunderstanding this but i have entered the command below and get this error, not sure what i am missing.

scifi map -c /scifi/config/default.yaml --input-bam-glob PD212_scifi_1N_4lines_7650_nuclei.bam /metadata/sciRNA-seq.PD212_scifi_1N_4lines_7650_nuclei.csv

scifi:pipeline:L141 (main) [INFO] > scifi-RNA-seq pipeline Traceback (most recent call last): File "/home/jsmith03/.local/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3361, in get_loc return self._engine.get_loc(casted_key) File "pandas/_libs/index.pyx", line 76, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 108, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 5198, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 5206, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'species_mixing'

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/home/jsmith03/.local/bin/scifi", line 33, in sys.exit(load_entry_point('scifi', 'console_scripts', 'scifi')()) File "/data/scratch/DGE/DUDGE/MOPOPGEN/jsmith/scifi/scifiRNA-seq/build/lib/scifi/pipeline.py", line 164, in main df["species_mixing"].fillna(value=0).astype(bool) File "/home/jsmith03/.local/lib/python3.8/site-packages/pandas/core/frame.py", line 3455, in getitem indexer = self.columns.get_loc(key) File "/home/jsmith03/.local/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3363, in get_loc raise KeyError(key) from err KeyError: 'species_mixing'