Hello everyone, I am currently running datasets through the newest version of the ampliseq pipeline (2.16.1) which runs through but does not generate the overall_summary.tsv files. This is the message that I get after the pipeline finishes. WARN: [nf-core/ampliseq] No reports found from process 'MULTIQC' ERROR ~ Failed to invoke

workflow.onComplete

event handler -- Check script '/cfs/klemming/home/n/nicolai2/.nextflow/assets/nf-core/ampliseq/subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf' at line: 153 or see '.nextflow.log' file for more details Completed at: 06-Feb-2026 111422 Duration : 31m 20s CPU hours : 7.1 (48.4% cached) Succeeded : 6 Cached : 220 Is this a known bug? I believe I also had that with older versions of the pipeline last year. The script at line 153 is not really helpful and the nextflow.log file is quite overwhelming in size with respect to figuring out what is wrong ... I am running ampliseq like this: screen -S name pixi shell module load PDC apptainer nextflow run nf-core/ampliseq -r 2.16.1 -name Nicolai -profile pdc_kth -params-file nf-params.json --project naiss2025-22-1670 Thank you for your help!

Hi there, this isnt a known bug, at least not that I recall. Could you attach the .nextflow.log?

but does not generate the overall_summary.tsv files.

This file should be generated. the nf-params.json might help here, if you want to share that.

The .nextflow.log is in the attachment. My params.json looks like this: { "input": "manifest_BS.tsv", "skip_cutadapt": true, "outdir": "results_new2", "email": "nicolai.laufer@gu.se", "dada_ref_taxonomy": "sbdi-gtdb", "skip_qiime_downstream": true, "skip_barplot": true, "skip_abundance_tables": true, "skip_alpha_rarefaction": true, "skip_ancom": true, "skip_multiqc": true, "picrust": false } I also never get an email that the pipeline has finished btw

"skip_multiqc": true

could be related, let me check.

I saw that as well but when I remove that, I still get no overall_summary.tsv after the run has finished

While the test is running:

Feb-06 141339.945 [main] DEBUG nextflow.Nextflow - java.io.IOException: Cannot run program "sendmail": error=2, No such file or directory

Feb-06 141339.947 [main] DEBUG nextflow.Nextflow - Trying with mail instead of sendmail

that means no email can be send because there is no email program installed, as far as I can see

So, might it be because I run ampliseq via a pixi shell?

Not sure what a pixi shell is. The only additional information that I got from the log is that all seemed fine and then:

Failed to invoke `workflow.onComplete` event handler
java.lang.reflect.InvocationTargetException: null
[...]
Caused by: java.io.IOException: Stream closed
[...]

One other user here has recommended loading nextflow using pixi. Pixi is a management tool using the conda ecosystem where you canthen add e.g. nextflow and work with it. I ran ampliseq three times today. So, I am not sure whether it is the correct one, in the last one I removed the skip_multiqc. Nonetheless, in all runs I didnt get an overall_summary.tsv What would be another way of running ampliseq when working on PDC Dardel?

I have neither experience with pixi nor with Dardel. I recommend looking in more generalized channel or simply use the search function in the nf-core slack, maybe there are already helpful comments in other channels.

Is it possible to run a script to retroactively generate the overall_summary.tsv of a completed run?

Most, if not all, components of the overall_summary.tsv are saved in the results folder scattered in the folders of the individual steps. Because you skip cutadapt and most downstream steps, the file

dada2/DADA2_stats.tsv

should contain the numbers you might look for.