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medema-group / BiG-MAP

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Hi BiG-MAP team, #23

Open hildaha opened 1 year ago

hildaha commented 1 year ago

I am having a problem with running the BiG-MAP analysis module. The problem seems to be related the metadata 'sample type' Kindly assist.

my command

python3 BiG-MAP.analyse.py --explore --compare -B /home/hildaha/BiG-MAP/Analysis/results_Mapping/biom-results/BiG-MAP.map.meta.dec.biom -T metagenomic -M Amendment -g CF NCF -O /home/hildaha/BiG-MAP/Analysis/results_analysis/

Attached also is the metadata file I used in mapping module

metadata.txt

Here is the error I get.

__Loading biom file___ Traceback (most recent call last): File "BiG-MAP.analyse.py", line 1229, in main() File "BiG-MAP.analyse.py", line 1061, in main biom_dict, args.metagroup) File "BiG-MAP.analyse.py", line 153, in get_sample_type elif sample_type == (sample["metadata"]["SampleType"]).upper(): KeyError: 'SampleType'

akbrand6 commented 7 months ago

I'm not part of the team, and I don't really know what I'm doing. But I had the same issue, in my metadata file I had a column called sample-type. so of course it shows up in my .biom file. I changed sample-type to SampleType in my biom file and somehow that fixed it. I think it is looking for that specific format in the biom file.