Dear Sir,
I open Silva-128 Qimme release and then go to rep-set and then rep set 16S only and import 99-otus-16S.fasta file with the commands as follows;
qiime tools import **
–type ‘FeatureData[Sequence]’ **
–input-path silva_128_99_16S.fasta **
–output-path 99_otus.qza
For taxonomy I open Silva-128 Qimme release and then go to taxonomy\16S_only\99\ and import majority_taxonomy_all_levels.txt with the following commands;
qiime tools import **
–type ‘FeatureData[Taxonomy]’ **
–input-format HeaderlessTSVTaxonomyFormat **
–input-path majority_taxonomy_all_levels.txt **
–output-path ref-taxonomy.qza
As I have paired end reads, each read is about 300bp and I use the following commands with the primers provided by the company.
qiime feature-classifier extract-reads **
–i-sequences 99_otus.qza **
–p-f-primer CCTACGGRRBGCASCAGKVRVGAAT **
–p-r-primer GGACTACNVGGGTWTCTAATCC **
–o-reads ref-seqs.qza
Then I use the following commands to get my classifier as
qiime feature-classifier fit-classifier-naive-bayes **
–i-reference-reads ref-seqs.qza **
–i-reference-taxonomy ref-taxonomy.qza **
–o-classifier classifier.qza
To get taxonomy I used the following commands
qiime feature-classifier classify-sklearn **
–i-classifier classifier.qza **
–i-reads rep-seqs.qza **
–o-classification taxonomy.qza
However when to get taxonomy. qzv I got following errors;
qiime metadata tabulate **
–m-input-file taxonomy.qza **
–o-visualization taxonomy.qzv
“There was an issue with viewing the artefact taxonomy.qza as QIIME 2 Metadata:
CategoricalMetadataColumn does not support values with leading or trailing whitespace characters. Column ‘Taxon’ has the following value: 'D_0__Bacteria;D_1__Chlorobi;D_2__Chlorobia;D_3__Chlorobiales;D_4__OPB56;D_5__uncultured bacterium '”
Thank You
