Open
Description
Description of the bug
Error trying to run the workflow in test mode when using singularity.
Command used and terminal output
$ nextflow run nf-core/chipseq -profile test,singularity --outdir .
...
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/chipseq] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_CHIPSEQ:PREPARE_GENOME:GTF2BED (genes.gtf)'
Caused by:
Process `NFCORE_CHIPSEQ:PREPARE_GENOME:GTF2BED (genes.gtf)` terminated with an error exit status (255)
Command executed:
gtf2bed \
genes.gtf \
> genes.bed
cat <<-END_VERSIONS > versions.yml
"NFCORE_CHIPSEQ:PREPARE_GENOME:GTF2BED":
perl: $(echo $(perl --version 2>&1) | sed 's/.*v\(.*\)) built.*/\1/')
END_VERSIONS
Command exit status:
255
Command output:
(empty)
Command error:
INFO: Converting SIF file to temporary sandbox...
WARNING: Skipping mount /mnt/lustre/e1000/home/edg01/edg01/shared/software/singularity/conda-env/envs/singularity/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
INFO: Cleaning up image...
FATAL: container creation failed: mount /tmp/nextflow_test/work->/tmp/nextflow_test/work error: while mounting /tmp/nextflow_test/work: destination /tmp/nextflow_test/work doesn't exist in container
Work dir:
/tmp/nextflow_test/work/19/ff6617324984e5332e850ee712dc96
Container:
/tmp/nextflow_test/work/singularity/depot.galaxyproject.org-singularity-perl-5.26.2.img
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
-- 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 detailsRelevant files
No response
System information
N E X T F L O W version 25.04.3 build 5949
Running on HPC, local executor
singularity version 3.8.6
Red Hat Enterprise Linux release 8.1 (Ootpa) x86_64 GNU/Linux
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nf-core/chipseq v2.1.0-g76e2382
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Core Nextflow options
revision : master
runName : gigantic_murdock
containerEngine : singularity
launchDir : /tmp/nextflow_test
workDir : /tmp/nextflow_test/work
projectDir : /home/edg01/edg01/tbooth2/.nextflow/assets/nf-core/chipseq
userName : tbooth2
profile : test,singularity
configFiles :
Input/output options
input : https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/samplesheet/v2.1/samplesheet_test.csv
read_length : 50
outdir : .
Reference genome options
fasta : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa
gtf : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf
Process skipping options
skip_preseq : true
Institutional config options
config_profile_name : Test profile
config_profile_description: Minimal test dataset to check pipeline function
Max job request options
max_cpus : 2
max_memory : 6.GB
max_time : 6.h
Generic options
fingerprint_bins : 100