Dear Thermokarst,
Plugin Error while performing diversity analysis
I would like to add that, I have used the dereplicate command to generate the table.qza and rep-seq.qza files.
As I am working with publicly available dataset, dada2-denoising leads to sample loss (as quality of reads falls below 20).
Hence, for a uniformity I am using "Trimmomatic" for quality trimming.
After doing Trimmomatic, I am importing the files to convert to "qiime artifact" using the command.
qiime tools import --type 'SampleData[SequencesWithQuality]' \
--input-format SingleEndFastqManifestPhred33V2 \
--input-path ~/Metagenomics/Project/manifest-Project.tsv \
--output-path ~/Metagenomics/Project/se-demux-Project.qza;
qiime demux summarize \
--i-data ~/Metagenomics/Project/se-demux-Project.qza \
--o-visualization ~/Metagenomics/Project/se-demux-Project-summary.qzv;
Followed by I am using the dereplicate command as mentioned below to generate Table and rep seq file
qiime vsearch dereplicate-sequences \
--i-sequences /home/devika/Metagenomics/Project/se-demux-Project.qza \
--o-dereplicated-table /home/devika/Metagenomics/Project/table-trim-Project.qza \
--o-dereplicated-sequences /home/devika/Metagenomics/Project/rep-seq-trim-Project.qza ;
qiime feature-table summarize \
--i-table /home/devika/Metagenomics/Project/table-trim-Project.qza \
--o-visualization /home/devika/Metagenomics/Project/table-trim-Project.qzv \
--m-sample-metadata-file /home/devika/Metagenomics/Project/metadata-Project.tsv;
qiime feature-table tabulate-seqs \
--i-data /home/devika/Metagenomics/Project/rep-seq-trim-Project.qza \
--o-visualization /home/devika/Metagenomics/Project/rep-seq-trim-Project.qzv
I am performing diversity
qiime diversity core-metrics-phylogenetic \
--i-table table-dada2-Project.qza \
--i-phylogeny rooted-tree-Project.qza \
--p-sampling-depth 5342 \
--m-metadata-file metadata_Project.tsv \
--output-dir core-metrics-phylogenetic;
Error Encountering
Plugin error from diversity:
The table does not appear to be completely represented by the phylogeny.
Debug info has been saved to /tmp/qiime2-q2cli-err-0oopses9.log
I would also like to add that, the same diversity was working out perfectly when using dada2 to generate the table.qza
So is it something with the table.qza file generated with dereplicate command ?
Please let me know if I am not clear or share any more data.