Sorry to hear there are still issues, @prince. I'm currently traveling, so apologies for the delay in responding. If you'd like faster responses, it's helpful to provide exactly what data you used and commands you ran, so I can quickly try to reproduce the error on my computer. You should also include what versions of qiime2 and the plugin you are using.
I just ran the following command using the crc_metadata.tsv and crc_relative.qza files provided in @cdiener's workshop repo and did not get any errors. I'm using the 2019.1 version of q2-perc-norm on the 2019.1 version of qiime2.
qiime perc-norm percentile-normalize \
--i-table crc_relative.qza \
--m-metadata-file crc_metadata.tsv \
--m-metadata-column disease_state \
--m-batch-file crc_metadata.tsv \
--m-batch-column study \
--o-perc-norm-table percentile_normalized.qza
Lowering the OTU presence threshold to 0 is not really recommended. We discussed this on a previous post: Q2-perc-norm - reduction in taxa