Yes, Java error is gone, but now there's something else wrong that was fine before:

Command error:

INFO:  Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred

INFO:  Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred

INFO:  Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred

INFO:  Environment variable SINGULARITYENV_SNIC_TMP is set, but APPTAINERENV_SNIC_TMP is preferred

/bin/bash: line 9: .command.run: Permission denied

Guessing that I need to change my script then, how exactly?

Hi again, Working on Rackham/Uppmax, running nf-core rnaseq. What do I need to do when I get

Disk quota exceeded

failure? I thought it meant that I have physically run out of storage space, but that is not the case (allocation on Crex is 1000 GB, current usage 34.7%, according to Naiss). I have, however, apparently used 760% of my 1000 core-hours for the month, so evidently I severely underestimated how much I was going to need, but it keeps going regardless?!

A reminder that NBIS has a bioinformatics drop-in Tuesdays at 14.00 ( so starting soon ) if you want some in person support, which includes getting support for running workflows on the Swedish HPCs http://meet.nbis.se/dropin

Did something happen on Rackham? It won't launch Nextflow. Slurm.out:

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
slurm-55758718.out (END)

sbatch script:

#!/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 xxx

Reminder: Today at 14.00

Hi, I hope it's okay to ask my stupid questions here. I tried to run the nascent pipeline on Dardel recently, but it could not be executed successfully. I used the following code: export NXF_SINGULARITY_CACHEDIR=/path/to/my/dir/ module load PDC java singularity nextflow run nf-core/nascent -profile pdc_kth --project=naiss2025-22-154 --input /cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/combine/Proseq1.csv --outdir /cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/result1/ --email tarazhang@foxmail.com --assay_type PROseq --genome GRCm38 -r 2.3.0 -work-dir /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/ --save_reference FALSE --scratch=TRUE The pipeline will always encounter some error and shows the information below ERROR ~ Error executing process > 'NFCORE_NASCENTNASCENTCOVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (SA_5m_REP3)' Caused by: Process

NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (SA_5m_REP3)

terminated for an unknown reason -- Likely it has been terminated by the external system Command executed: bedtools \ genomecov \ -ibam SA_5m_REP3.sorted.bam \ -bg -strand - \ | bedtools sort \ > SA_5m_REP3.minus.bedGraph cat <<-END_VERSIONS > versions.yml "NFCORE_NASCENTNASCENTCOVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS": bedtools: $(bedtools --version | sed -e "s/bedtools v//g") END_VERSIONS Command exit status: - Command output: (empty) Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred INFO: fuse2fs not found, will not be able to mount EXT3 filesystems INFO: gocryptfs not found, will not be able to use gocryptfs Work dir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/56/e86e77f3009640f45b17b64a3f87f1 Container: /cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-bedtools-2.31.1--hf5e1c6e_0.img Tip: you can replicate the issue by changing to the process work dir and entering the command

bash .command.run

-- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details ERROR ~ Failed to invoke

workflow.onComplete

event handler -- Check script '.nextflow/assets/nf-core/nascent/subworkflows/local/utils_nfcore_nascent_pipeline/main.nf' at line: 130 or see '.nextflow.log' file for more details I checked the log, and it didn't give me any useful information. It would be much appreciated if someone could help me solve this issue.

Nextflow's going to introduce some stricter syntax over time. Sweden's nf-core institutional profiles will need updating to meet these standards. Would someone be able to test the

pdc_kth

changes I've made please to make sure it works for others please? I've already tested, but it would be nice to make sure it works for someone else. https://github.com/nf-core/configs/pull/913

Hi, I am trying to run the nf-core/scrnaseq pipeline on Dardel. Below is the command I used: ./nextflow run nf-core/scrnaseq --input ./samplesheet.csv --outdir ./results --fasta /cfs/klemming/projects/supr/naiss2025-23-256/indranil/Genome_V2/genome.fa --gtf /cfs/klemming/projects/supr/naiss2025-23-256/indranil/Genome_V2/genes.gtf --aligner cellranger -profile pdc_kth --project=naiss2025-22-666 Before running this, I loaded the following modules: module load PDC java singularity I also downloaded Nextflow following the instructions on this page: https://nf-co.re/configs/pdc_kth/ Initially, the pipeline started correctly. When I ran ‘squeue --me’, I noticed several processes were queued and two were actively running. Nextflow also created several files in results and work directory. However, after 1–2 hours, the pipeline appeared to stop without any error messages. When I checked ‘squeue --me’ again, it still listed several queued processes, but none were running. Now its almost 6-7 hours but the queue status is still the same. I would appreciate your help in understanding what might have gone wrong or how I can debug this. Thank you!

Hi, I am quite new to nextflow and am trying to run the cutandrun worklow through UPPMAX. I can load the pipeline and manages to run this test sucessfully nextflow run nf-core/cutandrun -profile test However, whenever I run the following code through uppmax I encounter this error. nextflow run nf-core/cutandrun \ -profile uppmax,test \ --input 250717_sample_sheet_cutandrun.csv \ --outdir ./results \ --project uppmax xxxxx WARNING: Could not load nf-core/config profiles: https://raw.githubusercontent.com/nf-core/configs/master/nfcore_custom.config ERROR ~ No such file or directory: Config file does not exist: https://raw.githubusercontent.com/nf-core/configs/master/conf/conf/test.config Happy for any suggestions, thanks 🙂

Hi, I am trying to run Metadenovo on Dardel. I am stuck at the megahit assembly step getting the following error: Caused by: Process

NFCORE_METATDENOVO:METATDENOVO:MEGAHIT_INTERLEAVED (megahit_assembly)

terminated for an unknown reason -- Likely it has been terminated by the external system. So I was trying to include a config file as I thought it might be similar to the problem I have read here before. There I specified: process { withName: NFCORE_METATDENOVOMETATDENOVOMEGAHIT_INTERLEAVED { memory = 500.GB time = 2.d } but I still get the same error at the end. Is there anything I should change? Or did I do something wrong here? Thanks for your help!

I can't connect to Dardel at least since Wednesday evening, and the homepage (https://www.pdc.kth.se/) times out. Anyone else experiencing this?

Hello, I've been using nf-core pipelines on Dardel by running this before the pipeline: pixi shell screen -S name module load PDC apptainer It has been working for a while, but now this happens: (base) nicolai2@login1:/cfs/klemming/projects/snic/naiss2023-22-1217/ampliseq_analysis> pixi shell WARNING: Did not detect successful shell initialization within 3 second(s). Please check on https://pixi.sh/latest/advanced/pixi_shell/#issues-with-pixi-shell for more tips. . /tmp/pixi_env_sAH.sh (base) nicolai2@login1:/cfs/klemming/projects/snic/naiss2023-22-1217/ampliseq_aalysis> . /tmp/pixi_env_sAH.sh PIXI_SHELL_ACTIVATION_DONE (ampliseq_analysis) (base) nicolai2@login1:/cfs/klemming/projects/snic/naiss2023-22-1217/ampliseq_analysis> Does anyone have the same problem? Are there other ways and modules to load nextflow, so I can run the ampliseq pipeline? Kind regards, Nicolai

Courtesy of @Edmund: https://terminaltrove.com/turm/

hey! i've been trying to use the profile uppmax on bianca, nextflow version 25.10.2, but it says: WARNING: Could not load nf-core/config profiles: https://raw.githubusercontent.com/nf-core/configs/master/nfcore_custom.config WARNING: Could not load nf-core/config/viralrecon profiles: https://raw.githubusercontent.com/nf-core/configs/master/pipeline/viralrecon.config Unknown configuration profile: 'uppmax'

Hi, does any know if I installed some R packages on Dardel, are they transferrable and useable to Bianca like those in Rackham? Thank you

Hi, I am running the nf-core/pixelator pipeline (v2.3.1) on the Bianca (UPPMAX) cluster with 8 samples and facing persistent issues with high-memory steps. I initially tested the pipeline with a single sample, and it completed successfully. However, when running with multiple samples, some processes (especially nf-NFCORE_PIXELATOR_PIXEL / PIXELATOR_PNA_GRAPH) frequently fail with exit status 137 (out-of-memory) on standard nodes. To address this, I tried requesting fat nodes (mem256GB). But I started encountering submission errors such as: “Error submitting process … Execution is retried” In this situation, only the main job runs, while the sub-processes remain pending or repeatedly retry. As a result, the pipeline does not progress. I would appreciate your guidance on the following: 1. What is the recommended way to run nf-core/pixelator on Bianca when more than 128 GB memory is required? 2. Are there any special settings needed for running this pipeline on fat nodes with Nextflow/Slurm? Thank you very much in advance for your support. Best regards, Indranil

I'm running this workflow: https://pipelines.tol.sanger.ac.uk/genomeassembly using the

pdc_kth

profile. I'm srun-ing the main process. For a task using a local executor (

SANGERTOL_GENOMEASSEMBLY:GENOMEASSEMBLY:NUCLEAR_ASSEMBLY:INDEX_STAGE

) I keep getting the error

Process requirement exceeds available memory -- req: 6 GB; avail: 1.6 GB

. My guess is that this is caused by the

pdc_kth

profile requiring a minimum of 6GB of memory. Is this correct? What is the best way to handle this? The task itself seems to be very computationally light, so I can understand why it is run locally. Right now my workaround is srun-ing and asking for 6GB of memory, but that means requesting more resources than necessary for several days of run time which seems wasteful.

Hi I am running

nf-core/viralrecon

on Bianca, but it seems that the Bianca compute nodes are down. Is anyone else experiencing this?

jobinfo -u lili

CLUSTER: bianca
Running jobs:
   JOBID PARTITION                      NAME     USER          ACCOUNT ST          START_TIME  TIME_LEFT  NODES CPUS NODELIST(REASON)

Nodes in use:                              0
Nodes in devel, free to use:               0
Nodes in other partitions, free to use:    0
Nodes available, in total:                 0

Waiting jobs:
   JOBID    POS PARTITION                      NAME     USER          ACCOUNT ST          START_TIME   TIME_LEFT PRIORITY CPUS NODELIST(REASON)     FEATURES DEPENDENCY
      14      3      core nf-NFCORE_VIRALRECON_VIRA     lili  ProjID PD                 N/A     4:00:00   100000    1 (ReqNodeNotAvail          cpu (null)
      15      4      core nf-NFCORE_VIRALRECON_VIRA     lili  ProjID PD                 N/A     4:00:00   100000    1 (ReqNodeNotAvail          cpu (null)
      16      5      core nf-NFCORE_VIRALRECON_VIRA     lili  ProjID PD                 N/A     4:00:00   100000    1 (ReqNodeNotAvail          cpu (null)
      17      6      core nf-NFCORE_VIRALRECON_VIRA     lili  ProjID PD                 N/A     4:00:00   100000    1 (ReqNodeNotAvail          cpu (null)

Hi! I am new to using an nf-core pipeline on PDC, mores specifically nf-core/pangenome. I tried to use the pdc_kth config file but run into some problems, which seems to have to do with Nexflow itself. I tried to use the nextflow/26.04.3 module, would you say it's preferable to download nextflow instead and put it into bin?

Another question: It fails towards the end where I get an error that the disk quota is exceeded and I think it's about the singularity cache

Hi! I am running nf-core/viralrecon on Bianca but I keep on getting:

No space left on device

#!/usr/bin/env bash

#SBATCH -A naiss2026-4-549
#SBATCH -p core
#SBATCH -n 2
#SBATCH -t 10-00:00:00
#SBATCH -J sars-cov2-screening
#SBATCH -o slurm_log/%x_jobID_%j.out
#SBATCH -e slurm_log/%x_jobID_%j.err

module load bioinfo-tools Nextflow/latest

export NXF_VER=25.04.8 # version 25.10 cause the error: ERROR ~ Conversion = '4'

cd /proj/naiss2026-4-549/nobackup/analysis

params_file=/proj/naiss2026-4-549/assets/viralrecon_params.yml
config_file=/proj/naiss2026-4-549/assets/uppmax.config

samplesheet=$1
output_dir=$2
work_dir=$3

nextflow run /proj/naiss2026-4-549/assets/nf-core-viralrecon_3.0.0/3_0_0/main.nf \
 --project naiss2026-4-549 \
 -params-file $params_file \
 -c $config_file \
 --input $samplesheet \
 --outdir results/screening/$output_dir \
 -work-dir viralrecon_work_dir/$work_dir

And then submitting with:

sbatch viralrecon_screening_slurm.sh test_batch_samplesheet.csv test_batch_results_config test_batch_work

The project has plenty of available space and I am a bit unsure of where I should look at. Any ideas?

I have a colleague who has about 1TB sequencing data on UppMax that she needs to share with reviewers for a paper submission review stage... What would everyone here recommend for such a semi controlled access data share?

Hiya, this is a very inane question but I can't figure out from the Pelle documentation how to transfer files to Dardel??

Hi! Had an issue a couple of months ago when running nf-core/ampliseq on PDC's Dardel. I ran ampliseq v2.17.0 in screen as follows (Nextflow v25.10.4):

nextflow run nf-core/ampliseq \
  -r 2.17.0 \
  -params-file nf-params.json \
  -profile pdc_kth \
  -work-dir $SCRATCH/nxf_work \
  --project naiss2025-xx-yyyy \
  -c pull_timeout_retry.config \
  -resume

Got contacted by the PDC team that the pipeline had launched multiple java processes on the node where the pipeline was started, which triggered the center alert for using too much resources on the login node. Possible cause - CPU demanding local tasks. They were a bit surprised that this happened. I ran it with -profile pdc_kth which should submit the run to slurm and not run anything locally, right? Suggested solution: run via

salloc -p shared --nodes=1 -t 48:00:00

or

sbatch  -p shared --nodes=1 -t 48:00:00

Just wanted to inform the community that this issue came up!

Hi! I'm running into an issue with the pdc_kth profile I believe. I've previously been running amliseq through Nextflow on Dardel without issues, but when trying to run the following:

nextflow run nf-core/ampliseq \
-profile pdc_kth \
-r 2.17.0 \
-params-file params.yaml \
-bg

I get the following error message. Has there been any changes to the PDC profile config file, or what could be the reason? Thanks in advance! 🙏

Error nextflow.config:26:23: Unexpected input: '\n'
? 26 |     case "dardel":
?   |            ^
ERROR ~ Config parsing failed

With arrhenius being inaugurated soon, I guess it's time to fix a profile for use on that as well. An issue is that I don't have access (NBIS has historically been able to get projects for testing and so on, but that seems to not be the case now). Pavlin helps a bit, though so I think I can set up something. But we come back to naming, when we added dardel support we continued the convention from uppmax with a site/organisation rather than cluster-specific configs. I'm leaning towards continuing this and simply adding a

naiss

profile (that can then figure out where it's run and call on the specific profile, similar to what Mahesh fixed for uppmax. Anyone objects to a

naiss

profile?

Hi! I'm trying to run nf-core/magmap from Dardel and ran into some issues. I started with

nextflow pull nf-core/magmap

which worked fine. I continued with

nextflow run nfcore/magmap -r 1.2.0 -params-file params.yaml -profile pdc_kth

and got the following error:

Pulling nfcore/magmap ...
WARN: Cannot read project manifest -- Cause: Remote resource not found: <https://api.github.com/repos/nfcore/magmap/contents/nextflow.config>
Remote resource not found: <https://api.github.com/repos/nfcore/magmap/contents/main.nf>

I saw a similar issue here: nf-co.re/docs/running/troubleshooting, hence I tried

rm -r ~/.nextflow/assets/nf-core/

but no luck. I tried it both during an interactive session and on the login node. I tried updating my nextflow installation as well. I activate singularity by running

ml PDC singularity

. I also tried

nextflow pull nf-core/magmap -r 1.2.0

but always the same error. Has anyone faced similar issues? I saw a similar post here: github.com/nf-core/mag/issues/338 that suggested a Firewall issue. Many thanks for any help.

I'm trying to run FCS-GX (github.com/ncbi/fcs) using >512GB memory on dardel. I'm running FCS-GX through the snakemake workflow GEP2. When FCS-GX has sufficient memory it should require less than an hour to run (github.com/ncbi/fcs/wiki/FCS-GX-troubleshooting). I have attempted requesting both 512GB and 880GB, but I keep getting >24h runtimes and the warning

Note: detected page-faults (disk-thrashing) - GX may run slowly.

from FCS-GX. Has anyone else had luck running FCS-GX on Dardel?

I have access to arrhenius now 🙂 Opinions on https://github.com/nf-core/configs/pull/1183 are welcome.

Hello, I've recently converted a Nextflow pipeline from relying on conda to containers (singularity/docker). Before the containerisation, the pipeline ran on Dardel, but the goal now is to run it on Miarka (Uppmax). When I tried running the new container-version on Dardel, I got some errors. It seems like the singularity image was successfully downloaded, but it could not get mounted with FUSE due maximum number of namespaces reached. Anyone here knows how to fix it? This is how the .command.err files all look like:

INFO:    Mounting image with FUSE.
[91mERROR  : Failed to create user namespace: maximum number of user namespaces exceeded, check /proc/sys/user/max_user_namespaces
[0m

And this is the trace-file from the run: