I am attempting a rerun now: cl/dr: ampliseq version failed to call specified database, might be issue with previous versioning. I have a question about ampliseq that I hope you can help with. nextflow v 25.10.2, ampliseq v 2.15.0 Back in Nov I had run ampliseq (2.12.0) with nextflow 25.4.7 and was able to use dada_ref_taxonomy: sbdi-gtdb, however I've updated to the above versions and now Dardel is failing to retrieved the figshare file.

Jan-30 14:22:30.752 [FileTransfer-2] WARN  nextflow.file.FilePorter - Unable to stage foreign file: <https://figshare.scilifelab.se/ndownloader/files/54036416> (try 3 of 3) -- Cause: Unable to access path: <https://figshare.scilifelab.se/ndownloader/files/54036416>

java.io.IOException: Unable to access path: <https://figshare.scilifelab.se/ndownloader/files/54036416>

at nextflow.file.http.XFileSystemProvider.readAttributes(XFileSystemProvider.groovy:464)

at java.base/java.nio.file.Files.readAttributes(Files.java:1851)

at nextflow.file.CopyMoveHelper.copyToForeignTarget(CopyMoveHelper.java:162)

at nextflow.file.FileHelper.copyPath(FileHelper.groovy:1014)

at nextflow.file.FilePorter$FileTransfer.stageForeignFile0(FilePorter.groovy:373)

at nextflow.file.FilePorter$FileTransfer.stageForeignFile(FilePorter.groovy:328)

at nextflow.file.FilePorter$FileTransfer.run(FilePorter.groovy:300)

at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)

at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)

at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)

at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)

at java.base/java.lang.Thread.run(Thread.java:833)

i reverted have tried re running the pipeline with the old versions and receive the same error. I've also tried downloading and manually uploading the files to dardel and directing ampliseq to use a custom DB, in both versions, and the override filed to initiate. I then changed to the Silva database and the pipeline completed properly, so I can al least start thinking about the downstream analyses and results. I'd really like to run my samples through sbdi-gtdb as that's the database i've used for a lot of my previous analyses and would like to be able to compare to previous studies. Do you have any idea why Dardel can't access the path to Scilife's figshare? -Anders Daniel Lundin [8:37 AM] This is a known problem in some versions of ampliseq. Pull the latest ampliseq version (2.16.1). (And post in the ampliseq channel of the nf-core slack next time so others also learn.)

As Daniel asked, is that also not working with the most recent version (2.16.1) for you? Database locations can change ovber time, links might change and must be updated, Therefore older versions might not always be able to access databases.

Currently running now. So far so good it seems

Hi! I am experiencing the same issue, but haven't managed to solve it. I am running nextflow with the dardel module nextflow, and the latest version available is 25.04.07. When I run more recent versions of ampliseq, it tells me

Nextflow version 25.04.7 does not match workflow required version: >=25.04.8

. Which versions of nextflow & ampliseq were you able to combine successfully?

@Karin Garefelt I've got nf v25.10.2 currently running that i brought in myself with amp v 2.16.1. i've been fighting with it a bit due to a very large dataset. Please let me know how your run turns out 🙂

@Anders Johnson Thanks for letting me know. The run is not finished yet but looks healthy and normal so far!