I'm trying to use Gneiss to run with my own data. The environment is qiime2-2018.4. I followed the tutorial's steps but when I tried to investigate the taxonomies from the balance with the command:
qiime gneiss balance-taxonomy
I got the following error message
Plugin error from gneiss: sequence item 0: expected str instance, float found.
The attachments are the input files. I wonder how to fix this problem. Thank you very much!
Hi there @zhang --- the error lies in your taxa file - it looks like the taxonomy you imported has four columns, but is missing the column headers for the last two columns. Take a look at your source data before importing into QIIME 2 and clean that up - either provide names for those columns, or, remove the extra columns. You will need to make sure that this is cleaned up prior to importing taxonomy. Here is what the file looked like when I loaded in my text editor (with whitespace highlighting on):
Also, at least one row has values in those last two columns:
Let us know how it goes!
Hi @thermokarst, you are right, the problem came from the taxonomy file. When I downloaded the example file in qiime2 tutorials and shifted the example file with my taxonomy data, it worked. Thank you very much!
Just a quick follow up - I just reviewed the code and I believe this is a bug - this file probably should’ve never been allowed to have been imported in the first place, due to the extra columns on the end. Issue for reference. No clue when this will land, but just wanted to let you know. Thanks for reporting!
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