I am running the quality control plugin on 12 custom mock community samples for norovirus. (qiime2/2021.2 on HPC cluster). When I run the following
qiime quality-control evaluate-taxonomy
I obtained the blank evaluate-taxonomy.qzv file attached. I have tried to include a sample id for extracting frequency data and obtain the following error ‘Cannot retrieve an element from an empty/null table’ . I have viewed the input files in R using qiimeR. the taxonomy files and relative feature table are not empty and contain the overlapping features. I have tried running the same command above using the collapsed relative frequency table but obtained similar output and ran at various depths. I have applied evaluate-seqs and evaluate-composition with some of the same input files and obtained expected outputs.
Current process cutadapt-demux-dada2 denoise-feature classifier skearn-decontam in R- filter rep-seq, dada2 output, taxonomy by ids of contaminants decontam- quality control plugin.
I would appreciate any guidance on how to make this feature work!