Mapping file or biom table passed contain no `source` samples.

[HeatherDeel-USDA]

Hello, I've been trying to use sourcetracker and keep getting the following error: "Mapping file or biom table passed contain no source samples.". My mapping file definitely contains a "SourceSink" column with each source and sink labeled, so I am wondering if this issue has something to do with my biom table.

My biom table was imported to QIIME2 as a QIIME2 artifact, filtered, and exported as a biom table, so I am not sure if this is a QIIME2 issue when exporting my biom table or if it is a sourcetracker issue with my mapping file.

Does anyone have some input on this?

Thank you! Heather Deel

[johnchase]

Hi @heatherdeel, are you able to provide a small sample of your data and the command that you are running? From what you've described it sounds like there may not be any sample identifiers describing source samples that are found in the biom table, but without seeing the data it is impossible to know for sure

[HeatherDeel-USDA]

Hello, Thank you for such a quick reply! Here, I have attached the mapping file I've been using in the command, and here is the command I ran:

sourcetracker2 gibbs -i table_sourcetracker.biom -m maps/bone_skin_soil_map_st_filtered.txt -o prop_source_in_sinks/

I've also attached the first few lines of data in my biom table.

Thanks so much for your help!

data_sample.txt

bone_skin_soil_map_st_filtered.txt

[HeatherDeel-USDA]

Ahh, looking at your edited comment that does seem to possibly be the case. It looks like for whatever reason my biom table only has my sink samples.

Thanks for your help!

[johnchase]

Great, glad that helped! If it turns out to not be the case feel free to reopen