Prevalence filtering issue

Hello,

I'm following the "Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses [version 2; referees: 3 approved]" to analyse my 454 sequence data. I followed DADA2 pipeline tutorial (https://benjjneb.github.io/dada2/tutorial.html) and fixed some commands according to the Q&A (https://benjjneb.github.io/dada2/faq.html).

After assigning taxonomy, I constructed phylogenetic tree using phangorn R package, and started prevalence filtering. But the abundance graph is not like Figure 3. I found that phangorn is not good for the large taxa (5238 taxa in my data), so I also tried RAxML to construct the tree (benjjneb/dada2#88).

But the result is same as above. How can I make a abudance graph like figure 3?
Let me know if I'm being unclear or you need more info.

Thank you,

Chaewon

I uploaded my R codes on the github repository as below.
All codes were based on F1000 and dada2 workflows.

https://github.com/cwshin/454-microbiome