Taxa filtering with SILVA taxonomy annotations


I am trying to filter my feature table by the significant taxa identified by ANCOM at level 7. I downloaded the CSV file of the ANCOM results, and I was hoping to pass the taxonomy results, e.g, “D_0__Bacteria;D_1__Bacteroidetes;D_2__Bacteroidia;D_3__Bacteroidales;D_4__Prevotellaceae;D_5__Prevotella 7;D_6__uncultured Prevotellaceae bacterium,…” into the --p-include field of the qiime taxa filter-table, but the syntax does not appear to correct/compatible, for example:

(qiime2-2017.12) [[email protected] microbiome_2017-7]$ nohup qiime taxa filter-table --i-table table.qza --i-taxonomy rep-seqs_99-1_taxonomy.qza --p-include D_0__Bacteria;D_1__Actinobacteria;D_2__Actinobacteria;D_3__Corynebacteriales;D_4__Corynebacteriaceae;D_5__Corynebacterium 1;D_6__Corynebacterium casei --o-filtered-table practice.qza &
nohup: ignoring input and appending output to ‘nohup.out’

[1]+ Exit 127 D_6__Corynebacterium casei --o-filtered-table practice.qza
-bash: D_1__Actinobacteria: command not found
-bash: D_2__Actinobacteria: command not found
-bash: D_3__Corynebacteriales: command not found
-bash: D_4__Corynebacteriaceae: command not found
-bash: D_5__Corynebacterium: command not found
[1] 35610
-bash: D_6__Corynebacterium: command not found
(qiime2-2017.12) [[email protected] microbiome_2017-7]$

I know from reading the filtering data tutorial that Greengenes taxonomy has its specific annotations for filtering, does SILVA has something similar? It’s also highly possible that this is user error! :slightly_smiling_face:

Thanks for the help!

Hey @Lexie_Keding,

It looks like the problem is your command doesn’t have quotations in it, so bash is seeing those semicolons in the taxonomy string as instructions for it, and then running more commands. Try this out:

nohup \
qiime taxa filter-table \
  --i-table table.qza \
  --i-taxonomy rep-seqs_99-1_taxonomy.qza \
  --p-include 'D_0__Bacteria;D_1__Actinobacteria;D_2__Actinobacteria;D_3__Corynebacteriales;D_4__Corynebacteriaceae;D_5__Corynebacterium 1;D_6__Corynebacterium casei' \
  --o-filtered-table practice.qza \

Note the single-quotes around your include argument.

Let me know if that works!

1 Like

Hi @ebolyen!

That works perfectly, thanks so much!

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