Plugin error from gneiss:cannot perform reduce with flexible type


(Riley) #1

When running gneiss balance-taxonomy, I receive the following error:
qiime gneiss balance-taxonomy
–i-table ~/Documents/AXRS/DADA2_merged/merged-table.qza
–i-tree ~/Documents/AXRS/ANCOM/hierarchy.qza
–i-taxonomy ~/Documents/AXRS/Taxonomy/taxonomy.qza
–p-taxa-level 5
–p-balance-name ‘y0’
–m-metadata-file ~/Documents/AXRS/RS_mappingfile_SCFAs_completed_study_only_w_clustresponders.tsv
–m-metadata-column pcaclust
–o-visualization ~/Documents/AXRS/ANCOM/pcaclust/taxa_summary.qzv

#Plugin error from gneiss:
** cannot perform reduce with flexible type**

I tried searching for this error but couldn’t find anything. It said it made an error log but I couldn’t find it in any of my directories. Any idea what might be causing this? Happy to provide more information if needed

(Nicholas Bokulich) assigned mortonjt #2

(Jamie Morton) #3

Hi @rlhughes - we need a little more information. Can you provide the artifacts you used in this command?

(Nicholas Bokulich) unassigned mortonjt #4

(Riley) #5

Just sent in direct message! Thank you

(Nicholas Bokulich) assigned mortonjt #6

(Jamie Morton) #7

Ok. Turns out that because the pcaclust column is made up of its rather than strings, there is some strange type conversion happening in matplotlib. The work around is to convert this column from ints [1, 2] to string (I. E. A, B)

(Matthew Ryan Dillon) unassigned mortonjt #8

(Riley) #9

I thought I indicated in the mapping file that these were categorical though with the #q2:types directive below the header. Am I doing this incorrectly?

(Jamie Morton) #10

Nah - this is a bug that needs to raised. The work around is stated above.

(Riley) #11

Ok thank you so much for your help!