Update
For anyone working at UseGalaxy.org with the Dada2 tools, there is a known issue impacting a few of the tools.
The problem is on our side! The job environment and tools all run on the server and this tool suite had a dependency problem identified last week. We are still working on the full correction at this ticket if anyone is interested in the details Wrong container used for `dada2-plotqualityprofile` · Issue #446 · galaxyproject/usegalaxy-playbook · GitHub
Meanwhile, the workaround is to use a prior version of the tool! You can load up the tool form, and navigate with the Versions menu at the top. One version back is enough! Then set the form with your options and rerun. FAQ: Changing the tool version
dada2: mergePairs Merge denoised forward and reverse reads(Galaxy Version 1.34.0+galaxy1)
The same advice would be recommended for any of the other tools in this suite that are failing with a reason similar to this in their Job Information Details page (under Standard Tool Error).
/corral4/main/jobs/076/019/76019214/tool_script.sh: line 10: R: not found
/corral4/main/jobs/076/019/76019214/tool_script.sh: line 11: Rscript: not found
If this was your problem @zahir please give this a try! If something else happened, you are still welcome to post back your specific error for feedback! 
XRef → Dada2: plotQualityProfile