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 @#$#@%# Ubuntu 24.04, and I need to run these before for nextflow to work:
Fix
sudo sysctl -w kernel.apparmor_restrict_unprivileged_unconfined=0
sudo sysctl -w kernel.apparmor_restrict_unprivileged_userns=0
Looking forward for your help to move on finishing the annotation. Just to remind, I am running InterproScan on workstation which has 32 GB of RAM, and 16 cores.
Hope you can help me fix this never-ending analysis - and no, I have access to a HPC but it uses old Linux libraries and many things that I try to run fail and I don't have external connectivity/Internet. I rely on my aforementioned laptop/workstation - where I have nextflow/apptatiner installed.
Hi,
I ran InterproScan6 with 16 parallel processes/cores laptop/workstation with Linux, 16 cores/ 32 GB RAM.
I used the following code:
It was running well and then I got this error:
I am adding the .nextflow.log file. It was confusing that it starts with .*
The command line error has this
nextflow.zip
My OS is the @#$#@%# 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.