Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host with or without metabolomics data
I ran AMON with the picrust2 predicted Ko's and the detected compound KEGG IDs. I was able to get an enrichment heat map and KEGG Mapper file. But when I added the Host KO's list and the corresponding KEGG FTP file, I ran into an error. It would be of great help, if you can kindly let me know your insights on this. Please find the command used and the error message for the same. Looking forward for the suggestions
Error message:
Tools/anaconda3/envs/AMON/lib/python3.9/site-packages/matplotlib_venn/_venn3.py:57: UserWarning: Circle B has zero area
warnings.warn("Circle B has zero area")
/Tools/anaconda3/envs/AMON/lib/python3.9/site-packages/matplotlib_venn/_venn3.py:61: UserWarning: Circle C has zero area
warnings.warn("Circle C has zero area")
Traceback (most recent call last):
File "/Tools/anaconda3/envs/AMON/bin/amon.py", line 74, in
main(kos_loc, output_dir, other_kos_loc, detected_compounds, name1, name2, keep_separated, samples_are_columns,
File "Tools/anaconda3/envs/AMON/lib/python3.9/site-packages/AMON/predict_metabolites.py", line 364, in main
pathway_enrichment_df = calculate_enrichment(cos_produced, pathway_to_compound_dict)
File "/Tools/anaconda3/envs/AMON/lib/python3.9/site-packages/AMON/predict_metabolites.py", line 243, in calculate_enrichment
enrichment_table['adjusted probability'] = p_adjust(enrichment_table.probability)
File "/Tools/anaconda3/envs/AMON/lib/python3.9/site-packages/AMON/predict_metabolites.py", line 38, in p_adjust
res = multipletests(pvalues, method=method)
File "/Tools/anaconda3/envs/AMON/lib/python3.9/site-packages/statsmodels/stats/multitest.py", line 147, in multipletests
alphacSidak = 1 - np.power((1. - alphaf), 1./ntests)
ZeroDivisionError: float division by zero
Dear Team,
I ran AMON with the picrust2 predicted Ko's and the detected compound KEGG IDs. I was able to get an enrichment heat map and KEGG Mapper file. But when I added the Host KO's list and the corresponding KEGG FTP file, I ran into an error. It would be of great help, if you can kindly let me know your insights on this. Please find the command used and the error message for the same. Looking forward for the suggestions
Thank you
command used: amon.py --gene_set Picrust2_metagenome_KO.txt --detected_compounds Human_mesured_metabolite_withKEGG_id.txt --other_gene_set Host_human_KO_id.txt -o Test_with_hsa_KO --ko_file_loc /AMON/HSA_GENES/hsa_link/hsa_ko.list
Error message: Tools/anaconda3/envs/AMON/lib/python3.9/site-packages/matplotlib_venn/_venn3.py:57: UserWarning: Circle B has zero area warnings.warn("Circle B has zero area") /Tools/anaconda3/envs/AMON/lib/python3.9/site-packages/matplotlib_venn/_venn3.py:61: UserWarning: Circle C has zero area warnings.warn("Circle C has zero area") Traceback (most recent call last): File "/Tools/anaconda3/envs/AMON/bin/amon.py", line 74, in
main(kos_loc, output_dir, other_kos_loc, detected_compounds, name1, name2, keep_separated, samples_are_columns,
File "Tools/anaconda3/envs/AMON/lib/python3.9/site-packages/AMON/predict_metabolites.py", line 364, in main
pathway_enrichment_df = calculate_enrichment(cos_produced, pathway_to_compound_dict)
File "/Tools/anaconda3/envs/AMON/lib/python3.9/site-packages/AMON/predict_metabolites.py", line 243, in calculate_enrichment
enrichment_table['adjusted probability'] = p_adjust(enrichment_table.probability)
File "/Tools/anaconda3/envs/AMON/lib/python3.9/site-packages/AMON/predict_metabolites.py", line 38, in p_adjust
res = multipletests(pvalues, method=method)
File "/Tools/anaconda3/envs/AMON/lib/python3.9/site-packages/statsmodels/stats/multitest.py", line 147, in multipletests
alphacSidak = 1 - np.power((1. - alphaf), 1./ntests)
ZeroDivisionError: float division by zero