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BeeCSI-Microbiome / taxonomic_profiling_pipeline

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None of ['sample'] are in the columns #5

Closed ropolomx closed 2 years ago

ropolomx commented 2 years ago

@jlobri reported seeing this error. Her config file is updated and points to the correct sample table file. I was able to reproduce the error in her folder. The line referred in the error was introduced in pull request #4 

Traceback (most recent call last):
  File "/home/AAFC-AAC/ortegapoloro/miniconda3/envs/snakemake3/lib/python3.9/site-packages/snakemake/__init__.py", line 593, in snakemake
    workflow.include(
  File "/home/AAFC-AAC/ortegapoloro/miniconda3/envs/snakemake3/lib/python3.9/site-packages/snakemake/workflow.py", line 1182, in include
    exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
  File "/isilon/lacombe-rdc/users/tranlan/cas_2020/Snakefile", line 10, in <module>
    ALL_FILES = [s+"_R1" for s in SAMPLE.index] + [s+"_R2" for s in SAMPLE.index]
  File "/home/AAFC-AAC/ortegapoloro/miniconda3/envs/snakemake3/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper
    return func(*args, **kwargs)
  File "/home/AAFC-AAC/ortegapoloro/miniconda3/envs/snakemake3/lib/python3.9/site-packages/pandas/core/frame.py", line 5451, in set_index
    raise KeyError(f"None of {missing} are in the columns")
KeyError: "None of ['sample'] are in the columns"
ropolomx commented 2 years ago

Root cause found: the file names in the sample table are incorrect. Once that table is updated, the workflow should run.

LLansing commented 2 years ago

I saw this error as well when there were spaces instead of tabs in the sample file.