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: Taxa Filtering issue
''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 Qiime2View, 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