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Sourmash "Warning, less than 50 percent..." is unclear #20

Open DataSpott opened 3 years ago

DataSpott commented 3 years ago

Transferred issue from genome-to-json, original openend by AgressiveHayBale: The "Warning, less than 50 percent could be taxonomically assigned to analysed genome" message is unclear when Sourmash produce distribution of organisms and Unknown/Not found is less than 50%(look at the example). Maybe change it to: ... could be taxonomically assigned to ONE genome...

Also would be nice to do smth if species are closely related e.g. same genus or species and it is obviously inability of Sourmash to pinpoint one best genus not a case of a multiple of organisms in a sample, maybe information text or warning message in such situation?

DataSpott commented 3 years ago

Changed the warning message to: "Warning, less than X percent of the analysed genome could be taxonomically assigned to an single organism:\nThe organism might not be a bacteria/archea, is completely unknown without any close relatives, or the sample contains lots of contamination." Bold written is the change. What do you think @AggresiveHayBale @replikation

AggressiveHayBale commented 3 years ago

I would just add something that if the result species are closeley related it means that Sourmesh cannot pinpoint the exact species/strain from the sequence.