Hello!
So when I try to filter for mitochondria and chloroplasts using the following command:
qiime taxa filter-table
–i-table idfilttable.qza
–i-taxonomy taxonomy.qza
–p-exclude mitochondria,chloroplast
–o-filtered-table 1907table.qza
I get this error message:
CategoricalMetadataColumn does not support values with leading or trailing whitespace characters. Column ‘Taxon’ has the following value: 'D_0__Bacteria;D_1__Bacteroidetes;D_2__Ignavibacteria;D_3__OPB56;D_4__uncultured bacterium ’
This bug has already been reported and there is a thread open in GitHub about it: https://github.com/qiime2/q2-types/issues/179
It was several times re opened in the forums: (Qiime taxa filter-table; leading or trailing whitespace characters , Error: Silva132 99% classifer, white space in taxa name) and the solution proposed in those cases is posted here: Qiime taxa filter-table error
So I followed the advice and ran:
qiime tools export taxonomy.qza \
--output-dir taxonomy-with-spaces
qiime metadata tabulate \
--m-input-file taxonomy-with-spaces/taxonomy.tsv \
--o-visualization taxonomy-as-metadata.qzv
qiime tools export taxonomy-as-metadata.qzv \
--output-dir taxonomy-as-metadata
qiime tools import \
--type 'FeatureData[Taxonomy]' \
--input-path taxonomy-as-metadata/metadata.tsv \
--output-path taxonomy-without-spaces.qza
I dont fully understand this export function, do you need to create a folder to which the content in the taxonomy.qza is exported to? Anyways, when I try to run it I get this error message:
Error: no such option: --output-dir
I thought if I created a folder called taxonomy-with-spaces it would be solved but I guess I simply dont understand this export function. I tried qiime tools export --help and saw the option presented there is --output-path instead of --output-dir but I just get the same error. Could you help me out please?
Best regards!