KeyError: "None of ['Sample'] are in the columns" when running MMETHANE

[Juan-Carlos-Gomez]

Hi, I am testing out MMETHANE on my shotgun metagenomics dataset. I am providing a species relative abundance table from Metaphlan4 along with a log-transformed metabolite table from metabolomics data. However, I encountered the following error when running the pipeline.

1. I installed MMETHANE in a conda environment (mmethane_env).
2. I ran the following command:
   python3 /wynton/group/lynch/software/mmethane/mmethane/run.py \ -c MMETHANE_config_v2.cfg \ -o /wynton/group/lynch/Metag_Processed/MAAP2_shotgun_metag_10282024/MMETHANE/output

Error message

/wynton/home/lynchlab/c-gomez/.conda/envs/mmethane_env/lib/python3.10/site-packages/torchdata/datapipes/init.py:18: UserWarning:
################################################################################
WARNING!
The 'datapipes', 'dataloader2' modules are deprecated and will be removed in a
future torchdata release! Please see meta-pytorch/data#1196
to learn more and leave feedback.
################################################################################

deprecation_warning()

Loading subject data
Traceback (most recent call last):
File "/wynton/group/lynch/software/mmethane/mmethane/run.py", line 22, in
ProcessData(config)
File "/wynton/group/lynch/software/mmethane/mmethane/utilities/data.py", line 57, in init
self.Y, self.subject_data, self.subject_IDs = self.load_subject_data(self.config['data'])
File "/wynton/group/lynch/software/mmethane/mmethane/utilities/data.py", line 281, in load_subject_data
subject_data = subject_data.set_index(
File "/wynton/home/lynchlab/c-gomez/.conda/envs/mmethane_env/lib/python3.10/site-packages/pandas/core/frame.py", line 6122, in set_index
raise KeyError(f"None of {missing} are in the columns")
KeyError: "None of ['Sample'] are in the columns"

Troubleshooting Steps Taken:

1. I checked my input files to ensure they have a "Sample" column and I verified that the config file correctly specifies the input file paths.

Please let me know if there are any specific formatting requirements for the input tables or if there's an issue with the way MMETHANE expects the "Sample" column to be formatted.

Thanks!