Dear technical staff, I have four batches of 16S sequencing data sets for one project. Therefore, I firstly used cutadapt demux-paired and cutadapt trim-paired to trim the seqs, and then used DADA2 to denoise them. Though the most of seqs were removed, I thought the remained reads would be enough …

Thanks for putting together such a clear and detailed question, @Moon ! [image] Moon: I observed the usage of memory, it turned out that it used more than 200GB memory, and still kept increasing. And when the memory was filled, the process was killed. Good sleuthing :male_detective:! This is,…

My version of qiime2 is the newest. 2020.11.0.dev0

@Moon , your cutadapt and DADA2 questions were unrelated to your alignment question, and have been moved to separate topics. Please give unrelated questions their own topics - it helps keep things tidy. Let us know how your experiments with parttree and fragment-insertion go. Good luck! Chris

Dear ChrisKeefe, you are right! Memory is not enough to deal with so much rep-seqs. And the large amount of rep-seqs is owing to the error in cutadapt step. I did not strip the primer completely.

[image] Moon: Is it because my rep-seqs containing too much seqs? Sounds like you were right too! Glad you got this all worked out. :slight_smile:

QIIME 2 Forum

Errors in the pipeline of DADA2, Fearture-table merge-seqs, and phylogeny align-to-tree-mafft-fasttree.

Technical Support