Issue with rarefied table\ sequencing depth

Technical Support
1

Hello,

I am trying to run this command in my qiime2:

qiime diversity core-metrics-phylogenetic \
--i-phylogeny rooted-tree.qza \
--i-table table.qza \
--p-sampling-depth 5000 \
--m-metadata-file metadata.tsv \
--p-n-jobs-or-threads 1 \
--output-dir core-metrics-results

I got the following error:

**The rarefied table contains no samples or features. Verify your table is valid and that you provided a shallow enough sampling depth.**

**Debug info has been saved to /var/folders/pq/2rvx277j7vq8z1tkbjypgzww0000gp/T/qiime2-q2cli-err-e60uj9r5.log**

Could you please help me with this?

Thank you

2

Hello!
Did you check the amount of features in your table (you should visualize it as .qzv file or create alpha rarefaction curves).
If all samples in your dataset have a sequencing depth lower than 5000 then they will be filtered out.
So, you can set --p-sampling-depth to lower value. But before it, check dada2 denoising stats to see if your samples contained small number of the reads at the begining or you lost most of them on filtering, merging or chimera removal steps.

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