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?

Can you show the actual error with some context?

I get this error during different processes:

cp: error writing './nextclade_sars-cov-2_MN908947_2026-04-21--09-39-50Z/CHANGELOG.md': No space left on device
 cp: failed to extend './nextclade_sars-cov-2_MN908947_2026-04-21--09-39-50Z/CHANGELOG.md': No space left on device

Work dir:
 /proj/xxxxx/nobackup/analysis/viralrecon_work_dir/test_batch_work/d7/a4b754c6e1a05612936857c764d58d

Container:
 /proj/xxxxx/assets/nf-core-viralrecon_3.0.0/singularity-images/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-52-52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa-data.img

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- 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 ~ Invalid method invocation `call` with arguments: [[MN908947.3]] (nextflow.util.ArrayBag) on _closure9 type

 -- 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
WARN: Killing running tasks (10)
[ea/5c2157] Submitted process > NFCORE_VIRALRECON:VIRALRECON:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (GCA_009858895.3_ASM985889v3_genomic.200409.fna)

or:

fastp --in1 sample_1.fastq.gz --in2 sample_2.fastq.gz --out1 sample_1.fastp.fastq.gz --out2 sample_2.fastp.fastq.gz --json sample.fastp.json --html sample.fastp.html --thread 6 --detect_adapter_for_pe --cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50 
 fastp v1.0.1, time used: 17 seconds
 ls: cannot access *.fail.fastq.gz: No such file or directory
 cp: error writing './sample.fastp.json': No space left on device
 cp: failed to extend './sample.fastp.json': No space left on device

Work dir:
 /proj/xxxx/nobackup/analysis/viralrecon_work_dir/test_batch_work/61/5f232b91234819f889506a3f756424

Thanks, it's clearly in the project space so that's useful information.

df /proj/xxx

Filesystem                                                               1K-blocks      Used  Available Use% Mounted on
10.0.88.26@o2ib,10.0.90.26@o2ib:10.0.88.27@o2ib,10.0.90.27@o2ib:/cygnus 5242880000 458327584 4784552416   9% /proj/xxxxx

Ok, I have a feeling you'll need to send a support request. One thing you can try, though - can you now create files there (both interesting if you can create many empty files (with

touch

) or with actual content.

Thank you! When you write to create files there, where do you mean? Under the project?

Yes and for simplicity in the task work directory where you saw it fail.

Thank you!!!

(if you run into issues with creating empty files, it's a hint you've run into your file quota which is often not as visible).

I see, thank you!!

Yes, they have zoom drop-ins on tuesdays (same time as NBIS). See https://www.uu.se/centrum/uppmax.

Great! Thank you so much!