nf-core/rnaseq v3.0
Run Name: sick_wozniak
nf-core/rnaseq execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: null.
The full error message was:
Error executing process > 'RNASEQ:PREPARE_GENOME:GTF2BED (ITAG2.3_genomic_Ch6.gtf)'
Caused by:
Failed to pull singularity image
command: singularity pull --name depot.galaxyproject.org-singularity-perl-5.26.2.img.pulling.1759152933155 https://depot.galaxyproject.org/singularity/perl:5.26.2 > /dev/null
status : 127
message:
bash: singularity: command not found
The workflow was completed at 2025-09-29T15:35:33.500+02:00 (duration: 26.2s)
The command used to launch the workflow was as follows:
nextflow run nf-core/rnaseq -profile genotoul -r 3.0 --input /work/user/fmt099/TP_nextflow/inputs.csv --fasta /work/user/fmt099/TP_nextflow/genome/ITAG2.3_genomic_Ch6.fasta --gtf /work/user/fmt099/TP_nextflow/annotation/ITAG2.3_genomic_Ch6.gtf --aligner star_rsem -c /work/user/fmt099/TP_nextflow/sm_config.cfg
Pipeline Configuration:
| revision | 3.0 |
|---|---|
| runName | sick_wozniak |
| containerEngine | singularity |
| launchDir | /work/user/fmt099/TP_nextflow |
| workDir | /work/user/fmt099/TP_nextflow/work |
| projectDir | /home/fmt099/.nextflow/assets/nf-core/rnaseq |
| userName | fmt099 |
| profile | genotoul |
| configFiles | /home/fmt099/.nextflow/assets/nf-core/rnaseq/nextflow.config, /work/user/fmt099/TP_nextflow/sm_config.cfg |
| input | /work/user/fmt099/TP_nextflow/inputs.csv |
| fasta | /work/user/fmt099/TP_nextflow/genome/ITAG2.3_genomic_Ch6.fasta |
| gtf | /work/user/fmt099/TP_nextflow/annotation/ITAG2.3_genomic_Ch6.gtf |
| save_reference | true |
| igenomes_ignore | true |
| aligner | star_rsem |
| config_profile_description | The Genotoul cluster profile |
| config_profile_contact | support.bioinfo.genotoul@inra.fr |
| config_profile_url | http://bioinfo.genotoul.fr/ |
| max_cpus | 48 |
| max_memory | 120 GB |
| max_time | 4d |
| Date Started | 2025-09-29T15:35:07.324+02:00 |
| Date Completed | 2025-09-29T15:35:33.500+02:00 |
| Pipeline script file path | /home/fmt099/.nextflow/assets/nf-core/rnaseq/main.nf |
| Pipeline script hash ID | 4b892cc54e3b768dca93d19da30a907a |
| Pipeline repository Git URL | https://github.com/nf-core/rnaseq |
| Pipeline repository Git Commit | 3643a94411b65f42bce5357c5015603099556ad9 |
| Pipeline Git branch/tag | 3.0 |
| Nextflow Version | 20.11.0-edge |
| Nextflow Build | 5448 |
| Nextflow Compile Timestamp | 16-11-2020 08:23 UTC |
nf-core/rnaseq