Anyone know what I did wrong with my archae analysis, using the SILVA database for archaea?

Anyone know what I did wrong with my archae analysis, using the SILVA database for archaea?

Because when validating the sequences obtained in qiime these turn out to be bacteria and not archaea. The validation was carried out in NCBI BLAST

qiime tools import --type ‘SampleData[SequencesWithQuality]’ --input-path secuencias --input-format CasavaOneEightSingleLanePerSampleDirFmt --output-path demux-single-end-todas16s.qza

qiime tools validate demux-single-end-todas16s.qza

qiime demux summarize --i-data demux-single-end-todas16s.qza --o-visualization demux-single-end-todas16s.qzv

qiime dada2 denoise-single –i- demultiplexed-seqs demux-single-end-todas16s.qza –p-trunc-len 440 –p-n-threads 0 –o-table table-dada2.qza –o-representative-sequences rep-seq-dada2-todas16s.qza –o-denoising-stats stats-dada2.qza

(qiime2-2019.4) osiris@osiris-Inspiron-7386:~/16s$ qiime tools import --type ‘FeatureData[Sequence]’ --input-path arqueas.fna --output-path reference_arqueas.qza

(qiime2-2019.4) osiris@osiris-Inspiron-7386:~/16s$ qiime feature-classifier extract-reads --i-sequences reference_arqueas.qza --p-f-primer CCTACGGGNGGCWGCAG --p-r-primer GACTACHVGGGTATCTAATCC --p-trunc-len 440 --o-reads ref-seqs-arqueas.qza

(qiime2-2019.4) osiris@osiris-Inspiron-7386:~/16s$ qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads ref-seqs-arqueas.qza --i-reference-taxonomy archaea_ncbi_rrna_tax.qza --o-classifier classifier_arqueas.qza

(qiime2-2019.4) osiris@osiris-Inspiron-7386:~/16s$ qiime feature-classifier classify-sklearn --i-classifier classifier_arqueas.qza --i-reads rep-seq-dada2-todas16s.qza --o-classification taxonomy_arqueas.qza

(qiime2-2019.4) osiris@osiris-Inspiron-7386:~/16s$ qiime taxa barplot --i-table table-dada2-todas16s.qza --i-taxonomy taxonomy_arqueas.qza --m-metadata-file sample-metadata.tsv --o-visualization taxa-bar-plots_arqueas.qzv

Hi @osidito91,
Check out this similar topic from today:

@SoilRotifer's advice is probably more relevant to your issue (issues with the database and extracting reads from the database) than the follow-up advice I gave in that topic about mixed-orientation reads (though that could definitely be the issue! check it out).

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