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biocore / q2-greengenes2

A QIIME 2 plugin for interaction with the Greengenes2 database
BSD 3-Clause "New" or "Revised" License
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No tips error trying to classify #13

Closed christineolson-ucsf closed 1 month ago

christineolson-ucsf commented 1 year ago

Hello, in trying to use Greengenes2 with a FeatureData[Sequence] object, I get the following error saying "no requested tips found", full error message also attached. Can you please help me resolve this? ![image](https://user-images.githubusercontent.com/91097042/ image (1) 219550993-ba1f3b3e-fbae-47ab-b22a-b7ab5a86e2d1.png)

christineolson-ucsf commented 1 year ago

Other image of command run and initial error: image (2)

wasade commented 1 year ago

Thanks @christineolson-ucsf! Could you tell me how the FeatureData[Sequence] artifact was constructed, and are these 16S V4?

I am very interested in improving the error messages the plugin produces, so I'm hoping to use this github issue to guide a data detection method to better inform users.

Ilaria-Pirona commented 1 year ago

I am having the same problem while running qiime greengenes2 taxonomy-from-table (qiime2-2022.8). I am trying to assing the taxonomy to my V3-V4 regions. I followed the tutorial at link and the first command of the section "If you have V4 data" did not raise errors.

wasade commented 1 year ago

Hi @Ilaria-Pirona,

What specific primers were used? The majority of the data placed with DEPP are derived from 515F-806R. If your primers are relative to other positions, then it is unlikely your ASVs will be represented. In that scenario, I recommend using the non-v4-16s action

ebadiea commented 9 months ago

I got the same error "No requested tips found" and don't know how to fix it

wasade commented 9 months ago

Thanks, @ebadiea. Can you describe the data, and the commands used?

wasade commented 1 month ago

Please reopen if this is still a problem