Error during dada2: mergePairs step in DADA2 16S Tutorial

usegalaxy.org support
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1

Hello
I am following the Building an amplicon sequence variant (ASV) table from 16S data using DADA2

I follow all the steps until Infer Sample Composition via dada2:dada
but crash into error at the Merge paired reads via dada2: mergePairs
I also use the same version if the tools mentioned in the tutorial

Any guidance or help to resolve this issue would be highly appreciated

Thanks

2

Welcome @zahir

Hopefully we can help!

A few questions

  1. Are you working with the tutorial data or your own data?
  2. Are you working at UseGalaxy.org or a different server?
  3. What is reported on your Job Information Details page for one of the red error datasets? Full input/parameter table and all logs (click to expand each).
  4. Have you tried a rerun yet? Use the rerun button and start up a duplicated run (to eliminate a transient cluster issue!).

If you would like to generate a share link to your history and post it back here in your reply, all of these details will be included! You can unshare after we are done.

Or, if you would like to try to solve this yourself first, I have two workflow invocations using the tutorial’s data and workflow. Comparing your error run to the same step of the workflow is one way to review – click on the i-info icon for each to see the inputs and parameters in a table.

I would suggest starting up the rerun first now, if you haven’t yet, then you can come back and post some details for troubleshooting in case it fails again.

Let’s start there, thanks! :slight_smile:

3

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! :slight_smile:

XRef → Dada2: plotQualityProfile