error with gneiss balance-taxonomy

Jewelna_Osei-Poku · August 4, 2019, 10:43am

I have used a collapse table get a gneiss dendrogram-heamap. However when I try to get the balance names using ‘gneiss balance-taxonomy’ command, I get the following error:

Plugin error from gneiss:

“None of [Index([‘D_0__Bacteria;D_1__Proteobacteria;D_2__Alphaproteobacteria;D_3__Rhizobiales;D_4__Rhizobiales Incertae Sedis;D_5__uncultured’,\n ‘D_0__Bacteria;D_1__Proteobacteria;D_2__Gammaproteobacteria;D_3__Betaproteobacteriales;D_4__B1-7BS;D_5__uncultured beta proteobacterium’,\n ‘D_0__Bacteria;D_1__Proteobacteria;D_2__Gammaproteobacteria;D_3__Betaproteobacteriales;D_4__Burkholderiaceae;’,\n 'D_0__Bacteria;D_1__Cyanobacteria;D_2__Oxyphotobacteria;D_3__Chloroplast;D_4__Tetradesmus obliquus;D_5’,\n ‘D_0__Bacteria;D_1__Planctomycetes;D_2__Planctomycetacia;D_3__Isosphaerales;D_4__Isosphaeraceae;’,\n 'D_0__Bacteria;D_1__Patescibacteria;D_2__ABY1;D_3__Candidatus Falkowbacteria;;’,\n ‘D_0__Bacteria;D_1__Planctomycetes;D_2__Planctomycetacia;D_3__Isosphaerales;D_4__Isosphaeraceae;D_5__uncultured’,\n ‘D_0__Bacteria;D_1__Bacteroidetes;D_2__Bacteroidia;D_3__Chitinophagales;D_4__Chitinophagaceae;D_5__uncultured’,\n ‘D_0__Bacteria;D_1__Proteobacteria;D_2__Alphaproteobacteria;D_3__Rickettsiales;D_4__Rickettsiaceae;D_5__Candidatus Megaira’,\n ‘D_0__Bacteria;D_1__Proteobacteria;D_2__Alphaproteobacteria;D_3__Acetobacterales;D_4__Acetobacteraceae;D_5__Roseomonas’,\n 'D_0__Bacteria;D_1__Actinobacteria;D_2__Actinobacteria;D_3__PeM15;D_4__metagenome;D_5’,\n ‘D_0__Bacteria;D_1__Proteobacteria;D_2__Gammaproteobacteria;D_3__Betaproteobacteriales;D_4__Rhodocyclaceae;D_5__C39’,\n ‘D_0__Bacteria;D_1__Bacteroidetes;D_2__Bacteroidia;D_3__Sphingobacteriales;D_4__Sphingobacteriaceae;D_5__Pedobacter’,\n ‘D_0__Bacteria;D_1__Actinobacteria;D_2__Actinobacteria;D_3__Micrococcales;D_4__Microbacteriaceae;D_5__Agromyces’,\n ‘D_0__Bacteria;D_1__Actinobacteria;D_2__Actinobacteria;;;’,\n 'D_0__Bacteria;D_1__Patescibacteria;D_2__WWE3;;;’,\n ‘D_0__Bacteria;D_1__Proteobacteria;D_2__Alphaproteobacteria;D_3__Sphingomonadales;D_4__Sphingomonadaceae;’,\n 'D_0__Bacteria;D_1__Proteobacteria;D_2__Alphaproteobacteria;D_3__Acetobacterales;D_4__Acetobacteraceae;’,\n ‘D_0__Bacteria;D_1__Bacteroidetes;D_2__Bacteroidia;D_3__Flavobacteriales;D_4__Flavobacteriaceae;D_5__Flavobacterium’,\n ‘D_0__Bacteria;D_1__Patescibacteria;D_2__Saccharimonadia;D_3__Saccharimonadales;D_4__uncultured bacterium SBR2013;D_5__’,\n ‘D_0__Bacteria;D_1__Bacteroidetes;D_2__Bacteroidia;D_3__Chitinophagales;D_4__Chitinophagaceae;D_5__Sediminibacterium’,\n ‘D_0__Bacteria;D_1__Proteobacteria;D_2__Alphaproteobacteria;;;’,\n 'D_0__Bacteria;D_1__Proteobacteria;D_2__Gammaproteobacteria;;;’,\n ‘D_0__Bacteria;D_1__Deinococcus-Thermus;D_2__Deinococci;D_3__Deinococcales;D_4__Deinococcaceae;D_5__Deinococcus’,\n ‘D_0__Bacteria;D_1__Chlamydiae;D_2__Chlamydiae;D_3__Chlamydiales;D_4__Simkaniaceae;D_5__uncultured’,\n ‘D_0__Bacteria;D_1__Actinobacteria;D_2__Actinobacteria;D_3__Micrococcales;D_4__Microbacteriaceae;D_5__Candidatus Aquiluna’,\n ‘D_0__Bacteria;D_1__Bacteroidetes;D_2__Bacteroidia;D_3__Chitinophagales;D_4__Chitinophagaceae;’,\n 'D_0__Bacteria;D_1__Chloroflexi;D_2__Anaerolineae;D_3__SJA-15;;’,\n ‘D_0__Bacteria;D_1__Planctomycetes;D_2__Planctomycetacia;D_3__Pirellulales;D_4__Pirellulaceae;D_5__Pirellula’,\n ‘D_0__Bacteria;D_1__Verrucomicrobia;D_2__Verrucomicrobiae;D_3__Verrucomicrobiales;D_4__Verrucomicrobiaceae;D_5__uncultured’,\n 'D_0__Bacteria;D_1__Cyanobacteria;D_2__Oxyphotobacteria;D_3__Chloroplast;;’,\n 'D_0__Bacteria;D_1__Proteobacteria;D_2__Gammaproteobacteria;D_3__Betaproteobacteriales;;’,\n ‘D_0__Bacteria;D_1__Actinobacteria;D_2__Actinobacteria;D_3__Micrococcales;D_4__Microbacteriaceae;D_5__Leucobacter’,\n ‘D_0__Bacteria;D_1__Proteobacteria;D_2__Alphaproteobacteria;D_3__Sphingomonadales;D_4__Sphingomonadaceae;D_5__Porphyrobacter’,\n 'D_0__Bacteria;D_1__Proteobacteria;;;;__’],\n dtype=‘object’, name=‘Feature ID’)] are in the [index]”

Could anyone help me figure out how to solve this?

Thanks

ebolyen · August 6, 2019, 9:53pm

Hey @Jewelna_Osei-Poku,

Would you be able to provide your full command? My hunch is that either something like a table is empty, or the IDs are now taxonomy and we don’t have a matching set of IDs anymore.

thermokarst · August 30, 2019, 6:26pm

A post was split to a new topic: gneiss balance-taxonomy & taxonomy issues

Jewelna_Osei-Poku · September 3, 2019, 7:47pm

Hello ebolyen,
Thanks for the reply. Kindly find below the sequence of commands:

qiime taxa collapse --i-table Analyses/table.qza --i-taxonomy Analyses/taxonomy_from_Hughes.qza --p-level 6 --o-collapsed-table Analyses/table_level_6.qza

qiime gneiss correlation-clustering --i-table Analyses/table_level_6.qza --o-clustering Analyses/gneiss_hierarchy.qza

qiime gneiss balance-taxonomy --i-table Analyses/table_level_6.qza --i-tree Analyses/gneiss_hierarchy.qza --i-taxonomy Analyses/taxonomy_from_Hughes.qza --p-balance-name ‘y0’ --m-metadata-file metadata.tsv --m-metadata-column Site_Mosquito --o-visualization Analyses/y0_summary.qzv

thermokarst · September 5, 2019, 4:32pm

Hi @Jewelna_Osei-Poku! Please see this response to a similar post: gneiss balance-taxonomy & taxonomy issues

Thanks!

system · October 6, 2019, 10:47pm

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