Taxa Filtering issue 2

[lautaro.rostoll]

Hello Everyone!
I am having an issue with the qiime taxa filter-table command. I am using qiime2-2021.2 installed on conda. I am running into the same issue from this post.

Specifically, my issue is with the --p-exclude parameter. I want to exclude certain taxa from my data set. The taxa filter command completes without throwing any errors; however, when I pop the barplot into QIIME 2 View, the taxa are still there.'

I tried doing what @Nicholas_Bokulich suggested on that post and changed my code accordingly, however, I still run into the same issue. The code runs well and without any errors, but when I open the taxa barplot, the taxa is still there.

Here is my code:

qiime taxa filter-table
--i-table trim-table1.qza
--i-taxonomy silva99-taxonomy1.qza
--p-mode exact
--p-exclude " d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculaceae;s__uncultured_bacterium , d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculaceae;__ , d__Bacteria;p__Firmicutes;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor;s__Flavonifractor_plautii , d__Bacteria;p__Firmicutes;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor;__ , d__Bacteria;p__Firmicutes;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__uncultured;s__Pseudoflavonifractor_sp. , d__Bacteria;p__Firmicutes;c__Clostridia;o__Peptostreptococcales-Tissierellales;f__Peptostreptococcales-Tissierellales;g__Peptoniphilus;__ , d__Bacteria;p__Firmicutes;c__Clostridia;o__Peptostreptococcales-Tissierellales;f__Peptostreptococcales-Tissierellales;g__Peptoniphilus;s__Peptoniphilus_asaccharolyticus, d__Bacteria;p__Firmicutes;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella;s__uncultured_bacterium , d__Bacteria;p__Firmicutes;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Howardella;s__Howardella_ureilytica , d__Bacteria;p__Firmicutes;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Howardella;s__Eubacterium_sp. , d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Alcaligenaceae;g__Oligella;s__Oligella_ureolytica , d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Alcaligenaceae;g__Oligella;s__Oligella_urethralis , d__Bacteria;p__Firmicutes;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetitomaculum;s__Lachnospiraceae_bacterium , d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Weeksella;s__Weeksella_sp. , d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium;__ , d__Bacteria;p__Firmicutes;c__Clostridia;o__Peptostreptococcales-Tissierellales;f__Peptostreptococcaceae;g__Filifactor;s__uncultured_bacterium, d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Globicatella;__ , d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Globicatella;s__uncultured_bacterium , d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__uncultured;s__Globicatella_sp. , d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Wohlfahrtiimonas;s__Wohlfahrtiimonas_chitiniclastica , d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Alcaligenaceae;g__Paenalcaligenes;s__Paenalcaligenes_hominis"
--o-filtered-table taxafiltered_table.qza

qiime taxa barplot
--i-table taxafiltered_table.qza
--i-taxonomy silva99-taxonomy1.qza
--m-metadata-file metadata.tsv
--o-visualization taxafiltered-bar-plot.qzv

I have been trying different things for a while and don't understand what the problem is.
Thanks!

Lautaro

[SoilRotifer (Mike Robeson)]

Hi @lautaro.rostoll,

It seems you have extraneous spaces in your --p-exclude string. For example, note the space right at the beginning after the first quote:

" d__Bacteria;...

Also, you should not have spaces between the commas of the different strings. That is:

...g__Muribaculaceae;s__uncultured_bacterium , d__Bacteria;p__Bacteroidota;...

should be:

...g__Muribaculaceae;s__uncultured_bacterium,d__Bacteria;p__Bacteroidota;...
etc...

See the example here

It also appears that you are copying the taxonomy from one of the taxonomy QZV visualizations. That is, the actual taxonomy strings do not contain ;__. This only appears in the visualizer as you select different rank depths. This simply conveys that there is no information at that level in the visualizer. More information can be found here:

Why does most my sample has uncategorized bacteria?

Hi @amm59063, Note the d__Bacteria;__;__;__;__;__;__ only appears in that form within the visualizer. So searching for that pattern will not work. The ;__;__;__;__;__;__ is simply filled in as you view more ranks in the visualizer. In actuality, the taxonomy information may only contain d__Bacteria. The best way to figure out what to search for is to make a sample_taxonomy_paired.qzv file and view that. I usually run something like this when filtering SILVA taxonomy: --p-mode 'contains' \…

Finally, why not use --p-mode contains? Then make your --p-exclude line be simply like:

--p-exclude "g__Muribaculaceae,f__Oscillospiraceae,Peptostreptococcales-Tissierellales,g__Howardella,g__Oligella,s__Lachnospiraceae_bacterium,f__Weeksellaceae,f__Aerococcaceae,s__Wohlfahrtiimonas_chitiniclastica,s__Paenalcaligenes_hominis"

or something similar to that. I may have missed a few... but you get the point.

[lautaro.rostoll]

Thanks so much!
I will give it a try and let you know how it goes!

[lautaro.rostoll]

It worked! Thank so much @SoilRotifer