I am running a rather large 16S data set using dada2 and the following command:
qiime dada2 denoise-paired --i-demultiplexed-seqs 16S_demux-paired-end.qza --o-table 16S_dada2_table --o-representative-sequences 16S_rep-seqs --p-trunc-len-f 250 --p-trunc-len-r 238 --verbose --p-n-threads 0 --p-n-reads-learn 2000000
I received this warning:
In dada(drpsF, err = NULL, selfConsist = TRUE, multithread = multithread) :
Self-consistency loop terminated before convergence.
I read on Github that this is not always a problem but you should check the error rates and see how close to convergence they are. Is this a function I can do in Qiime2 or only in the dada2 R package? Should I ignore it and continue on? Any suggestions or clarification would be great!