Emperor plot error with custom axis

Hi, I have a similar problem as what was discussed here: Emperor: custom axis and numeric data error but I have the latest version of QIIME 2 (QIIME 2 release: 2018.2 QIIME 2 version: 2018.2.0 q2cli version: 2018.2.0) so the solution found doesn’t help me.

When I run
qiime emperor plot
–m-metadata-file …/Aerobic-metadata-emp.tsv
–i-pcoa weighted_unifrac_pcoa_results.qza
–p-custom-axes IndivNum
–o-visualization weighted_unifrac_pcoa_indivnum.qzv

I get the error:
All values in a custom axis must be numeric, this summary shows the invalid values and the number of times they were found in column ‘IndivNum’:
NaN 1

I checked my metadata file in the IndivNum and they’re all number values… I even changed my ones into fours to see if that would help and it didn’t. Attached is my metadata file.

Thanks!Aerobic-metadata-emp.tsv (777 Bytes)

Hey there @Masha_T!

I took a look at your metadata file (thanks for attaching!), and I agree, nothing looks out of place there. The particular error you are reporting looks like it has to do with missing data, though - is it possible that there is a sample present in your weighted unifrac results that isn’t in your metadata? One way to check is to run feature-table summarize on the table used to generate that file (if it was generated as part of diversity core-metrics that table is save in the --o-rarefied-table value. Take a peek at that and let us know what you find! We will get to the bottom of this! :t_rex:

Yes this fixed the problem! Thank you very much for your advice, and just a shutout to this forum in general, I really appreciate the support that is provided here.



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