Did something happen on Rackham? It won't launch N...
# helpdesk-hpc-swedenj
Julia Griese
06/09/2025, 9:01 AMDid something happen on Rackham? It won't launch Nextflow.
Slurm.out:
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WARNING!!! Multiple pipelines are not compatible with the latest nextflow framework since version 25
Temporarily this module will load the latest compatible version 24.10.6 instead
Please use export NXF_VER=nextflow_version to select different version
<https://www.nextflow.io/docs/latest/config.html#environment-variables>
ls /sw/bioinfo/Nextflow/latest/rackham/nxf_home/framework/ to check the installed versions
Note that NXF_HOME is set to $HOME/.nextflow
Please change NXF_HOME to a place in your project directory (export NXF_HOME=yourprojectfolder)
WARNING: java.io.tmpdir directory does not exist
ESC[33mNextflow 24.04.5 is available - Please consider updating your version to itESC(BESC[m
/sw/bioinfo/Nextflow/latest/rackham/nextflow: line 175: exec: : not found
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#!/bin/bash -l
#SBATCH -A xxx
#SBATCH -p core
#SBATCH -n 2
#SBATCH -c 10
#SBATCH -t 4-00:00:0
#SBATCH -J nf-core
module load bioinfo-tools
module load Nextflow/latest
module load nf-core
module load nf-core-pipelines
export NXF_VER=24.10.6
export NXF_HOME=$PWD
export SINGULARITY_CACHEDIR=${PWD}/SINGULARITY_CACHEDIR
export SINGULARITY_TMPDIR=${PWD}/SINGULARITY_TMPDIR
export NXF_SINGULARITY_CACHEDIR=${SINGULARITY_CACHEDIR}
mkdir -p SINGULARITY_CACHEDIR SINGULARITY_TMPDIR
mkdir results_DSM40517_3
# nextflow drop nf-core/rnaseq
nextflow run nf-core/rnaseq -r 3.18.0 -c scripts/params_DSM40517_3.config -profile uppmax --project xxxp
Pavlin Mitev
06/09/2025, 9:09 AMcan you try again...
j
Julia Griese
06/09/2025, 9:11 AM Copy code
WARNING!!! Multiple pipelines are not compatible with the latest nextflow framework since version 25
Temporarily this module will load the latest compatible version 24.10.6 instead
Please use export NXF_VER=nextflow_version to select different version
<https://www.nextflow.io/docs/latest/config.html#environment-variables>
ls /sw/bioinfo/Nextflow/latest/rackham/nxf_home/framework/ to check the installed versions
Note that NXF_HOME is set to $HOME/.nextflow
Please change NXF_HOME to a place in your project directory (export NXF_HOME=yourprojectfolder)
bash: /sw/bioinfo/Nextflow/latest/rackham/nextflow: Permission deniedp
Pavlin Mitev
06/09/2025, 9:11 AMApparently there was an update on Jun 7 that broke stuff again...
😵 1
j
Julia Griese
06/09/2025, 9:11 AMI figured it would be something like that... 😵💫
Julia Griese
06/09/2025, 9:11 AMMy last successful run finished on june 6
p
Pavlin Mitev
06/09/2025, 9:12 AMOr rather the fixes that worked before are not working anymore ;-( and the update is done every night automatically...
j
Julia Griese
06/09/2025, 9:15 AMSo I wait for a fix...?
p
Pavlin Mitev
06/09/2025, 9:16 AMIt looks working again - please try
j
Julia Griese
06/09/2025, 9:17 AMNope
bash: /sw/bioinfo/Nextflow/latest/rackham/nextflow: Permission deniedp
Pavlin Mitev
06/09/2025, 9:18 AMHow about now 😇
j
Julia Griese
06/09/2025, 9:29 AMYes, now it's running 🙂 Thank you!
p
Pavlin Mitev
06/09/2025, 9:30 AMWe need to solve this better on the new cluster ...
😅 1
party this 1
m
Matthias Zepper
06/09/2025, 9:52 AMDoes this slightly melodramatic text pertain to the
process.shell Copy code
WARNING!!! Multiple pipelines are not compatible with the latest nextflow framework since version 25
Temporarily this module will load the latest compatible version 24.10.6 insteadj
Julia Griese
06/09/2025, 9:54 AMI think so. This message started showing up after we discovered that issue (I was apparently one of the first affected users and we spent quite a bit of time figuring out what the problem was).
p
Pavlin Mitev
06/09/2025, 10:05 AMI agree, the "fix" is temporary... The problem is that our users wants to run the same pipeline until they finish the project and that often could be some years... I will replace the warning, switch back to the latest release and @Julia Griese please use the easiest fix in your case
export NXF_VER=24.10.6j
Julia Griese
06/09/2025, 10:06 AMYes, that's what I'm doing 🙂
👍 1
m
Matthias Zepper
06/09/2025, 10:16 AMI will replace the warningI didn’t mean to instigate this. It is good to warn users clearly, since we regularly see people seeking help with that problem still. Just the combination of the atwitter tone and your remark Apparently there was an update on Jun 7 that broke stuff again... made me wonder what I missed. 😄