Problems running v0.8.0 using nextflow v0.25 (in nf-core-3.2.1-0)

[gitcruz]

Description of the bug

Hi,

I installed v0.8.0 and nf-core-3.2.1-0 conda environment (that contains nextflow v0.25.04.2.5947). However I am getting the following error, is this due to any incompatibility? It seems that the problem points to the singularity image...

I am pasting below the last lines of .nextflow.log:

May-27 11:04:41.175 [main] ERROR nextflow.Nextflow - Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
May-27 11:04:41.178 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: slurm) - terminating tasks monitor poll loop
May-27 11:04:41.204 [Actor Thread 2] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:GENERATE_CONFIG; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
May-27 11:04:41.213 [Actor Thread 15] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=docker://docker.io/genomehubs/blobtoolkit:4.4.6; path=/software/assembly/pipelines/nf-core-pipelines/singularity/cache/docker.io-genomehubs-blobtoolkit-4.4.6.img
May-27 11:04:41.233 [Actor Thread 15] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
May-27 11:04:41.233 [Actor Thread 4] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
May-27 11:04:41.233 [Actor Thread 16] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
May-27 11:04:41.229 [main] ERROR nextflow.cli.Launcher - @unknown
java.util.ConcurrentModificationException: null
        at java.base/java.util.ArrayList$Itr.checkForComodification(ArrayList.java:1013)
        at java.base/java.util.ArrayList$Itr.next(ArrayList.java:967)
        at nextflow.Session.callIgniters(Session.groovy:545)
        at nextflow.Session.fireDataflowNetwork(Session.groovy:539)
        at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:250)
        at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:139)
        at nextflow.cli.CmdRun.run(CmdRun.groovy:379)
        at nextflow.cli.Launcher.run(Launcher.groovy:513)
        at nextflow.cli.Launcher.main(Launcher.groovy:673)

Do you have any idea on how could I fix this?

Thanks

[muffato]

Hi @gitcruz

Sorry I haven't responded earlier. Some crazy things happened here.
No it's not something I've seen before.
Did you find a solution ?

[gitcruz]

No, we haven't find any solution. So far we are using v0.6.0 that is in Sync with our current assembly pipeline version. But soon we will do a Major upgrade including BUSCO v5.8.2 and I would like to have nexflow pipeline v0.8.0 ready. @muffato, I will ask the Sysadmin if there's something on our end that produce the error to open the docker image with our singularity... If you have any sugestion, let me know. Thanks, Fernando El lun, 23 jun 2025, 10:24, Matthieu Muffato ***@***.***> escribió:

…

*muffato* left a comment (sanger-tol/blobtoolkit#185) <#185 (comment)> Hi @gitcruz <https://github.com/gitcruz> Sorry I haven't responded earlier. Some crazy things happened here. No it's not something I've seen before. Did you find a solution ? — Reply to this email directly, view it on GitHub <#185 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB34KVOKSX7D6ORJWB3LLUL3E62UJAVCNFSM6AAAAAB57PJ3NSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDSOJVGQZTINJXG4> . You are receiving this because you were mentioned.Message ID: ***@***.***>