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NextFlow ~Error executing process > 'INTERPROSCAN:COMBINE:XREFS_LOCAL (10)' Caused by: Java heap space | Ubuntu 24.04 #6989

@desmodus1984

Description

@desmodus1984

Hi,
I ran InterproScan6 with 16 parallel processes/cores laptop/workstation with Linux, 16 cores/ 32 GB RAM.

I used the following code:

nextflow run ebi-pf-team/interproscan6     -profile apptainer --goterms     --input LW3.fasta --pathways     --datadir data --max-workers 16

It was running well and then I got this error:
I am adding the .nextflow.log file. It was confusing that it starts with .*

The command line error has this

Plus 7 more processes waiting for tasks…
WARN: Killing running tasks (9)
ERROR ~ Unexpected thread exception

 -- Check '.nextflow.log' file for details
ERROR ~ Error executing process > 'INTERPROSCAN:COMBINE:XREFS_LOCAL (10)'

Caused by:
  Java heap space


Source block:
  String outputFilePath = task.workDir.resolve('matches2xrefs.json')
  ProcessXrefs.run(matches_path.toString(), db_releases, add_goterms, add_pathways, panther_paint_dir, outputFilePath)

Work dir:
  /home/jpac1984/work/fb/c934e285e3389674eb8f4fbf8680ab

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details

nextflow.zip

My OS is the @#$#@%# Ubuntu 24.04, and I need to run these before for nextflow to work:
Fix
sudo sysctl -w kernel.apparmor_restrict_unprivileged_unconfined=0
sudo sysctl -w kernel.apparmor_restrict_unprivileged_userns=0

Looking forward for your help to move on finishing the annotation. Just to remind, I am running InterproScan on workstation which has 32 GB of RAM, and 16 cores.

Hope you can help me fix this never-ending analysis - and no, I have access to a HPC but it uses old Linux libraries and many things that I try to run fail and I don't have external connectivity/Internet. I rely on my aforementioned laptop/workstation - where I have nextflow/apptatiner installed.

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