parabricks only works reliable with --no_intervals #2028
Description
Description of the bug
When I run version 3.6.0 with --aligner parabricks I always run into a bug which looks like this:
ERROR ~ Invalid method invocation `call` with arguments: [/mnt/lustre/groups/nahnsen/nahbu450/pm4onco/2025-10/sarek/seqc2-wes-work/8a/5fb9ec00951122e532ad33644cb617/chr2_16146120-32867130.bed, 21, /mnt/lustre/groups/nahnsen/nahbu450/pm4onco/2025-10/sarek/seqc2-wes-work/8a/5fb9ec00951122e532ad33644cb617/chr2_238904048-242183529.bed, 21, /mnt/lustre/groups/nahnsen/nahbu450/pm4onco/2025-10/sarek/seqc2-wes-work/8a/5fb9ec00951122e532ad33644cb617/chr4_10001-1429358.bed, 21, /mnt/lustre/groups/nahnsen/nahbu450/pm4onco/2025-10/sarek/seqc2-wes-work/8a/5fb9ec00951122e532ad33644cb617/chr12_37235253-37240944.bed, 21, /mnt/lustre/groups/nahnsen/nahbu450/pm4onco/2025-10/sarek/seqc2-wes-work/8a/5fb9ec00951122e532ad33644cb617/chr15_20729747-21193490.bed, 21, /mnt/lustre/groups/nahnsen/nahbu450/pm4onco/2025-10/sarek/seqc2-wes-work/8a/5fb9ec00951122e532ad33644cb617/chr7_58169654-60828234.bed, 21, /mnt/lustre/groups/nahnsen/nahbu450/pm4onco/2025-10/sarek/seqc2-wes-work/8a/5fb9ec00951122e532ad33644cb617/chr10_39590436-39593013.bed, 21, /mnt/lustre/groups/nahnsen/nahbu450/pm4onco/2025-10/sarek/seqc2-wes-work/8a/5fb9ec00951122e532ad33644cb617/chr8_44033745-45877265.bed, 21, /mnt/lustre/groups/nahnsen/nahbu450/pm4onco/2025-10/sarek/seqc2-wes-work/8a/5fb9ec00951122e532ad33644cb617/chr20_36314720-64334167.bed, 21, /mnt/lustre/groups/nahnsen/nahbu450/pm4onco/2025-10/sarek/seqc2-wes-work/8a/5fb9ec00951122e532ad33644cb617/chr4_190173122-190204555.bed, 21, /mnt/lustre/groups/nahnsen/nahbu450/pm4onco/2025-10/sarek/seqc2-wes-work/8a/5fb9ec00951122e532ad33644cb617/chr5_139453660-155760324.bed, 21, /mnt/lustre/groups/nahnsen/nahbu450/pm4onco/2025-10/sarek/seqc2-wes-work/8a/5fb9ec00951122e532ad33644cb617/chr6_95070791-167591393.bed, 21, /mnt/lustre/groups/nahnsen/nahbu450/pm4onco/2025-10/sarek/seqc2-wes-work/8a/5fb9ec00951122e532ad33644cb617/chr17_60001-448188.bed, 21, /mnt/lustre/groups/nahnsen/nahbu450/pm4onco/2025-10/sarek/seqc2-wes-work/8a/5fb9ec00951122e532ad33644cb617/chr1_122026460-124977944.bed, 21, /mnt/lustre/groups/nahnsen/nahbu450/pm4onco/2025-10/sarek/seqc2-wes-work/8a/5fb9ec00951122e532ad33644cb617/chr18_47019913-54536574.bed, 21, /mnt/lustre/groups/nahnsen/nahbu450/pm4onco/2025-10/sarek/seqc2-wes-work/8a/5fb9ec00951122e532ad33644cb617/chrX_37285838-49348394.bed, 21, /mnt/lustre/groups/nahnsen/nahbu450/pm4onco/2025-10/sarek/seqc2-wes-work/8a/5fb9ec00951122e532ad33644cb617/chr1_10001-207666.bed, 21, /mnt/lustre/groups/nahnsen/nahbu450/pm4onco/2025-10/sarek/seqc2-wes-work/8a/5fb9ec00951122e532ad33644cb617/chr11_51078349-54425074.bed, 21, /mnt/lustre/groups/nahnsen/nahbu450/pm4onco/2025-10/sarek/seqc2-wes-work/8a/5fb9ec00951122e532ad33644cb617/chr13_86252980-111703855.bed, 21, /mnt/lustre/groups/nahnsen/nahbu450/pm4onco/2025-10/sarek/seqc2-wes-work/8a/5fb9ec00951122e532ad33644cb617/chr9_41229379-41237752.bed, 21, /mnt/lustre/groups/nahnsen/nahbu450/pm4onco/2025-10/sarek/seqc2-wes-work/8a/5fb9ec00951122e532ad33644cb617/chrY_9055175-9057608.bed, 21] (nextflow.util.ArrayBag) on _closure7 type
-- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: [https://nf-co.re/docs/usage/troubleshooting](https://nf-co.re/docs/usage/troubleshooting)
-- Check '.nextflow.log' file for details
WARN: [nf-core/sarek] No reports found from process 'MULTIQC' -[nf-core/sarek] Sent summary e-mail to [email protected] (sendmail)
- -[nf-core/sarek] Pipeline completed with errors-
WARN: Killing running tasks (6)
WARN: Seqera Platform request field `workflow.errorMessage` exceeds expected size | offending value: `No signature of method: Script_6f9426fcbfcfb62d$_runScript_closure1$_closure2$_closure7.call() is ap(truncated)`, size: 442 (max: 255)
Command used and terminal output
nextflow run nf-core/sarek -r 3.6.0 -profile singularity \
--tools freebayes,muse,mutect2,strelka,varlociraptor,vep \
--aligner parabricks
--wesRelevant files
No response
System information
- Nextflow version: 24.10 and 25.04.6 / 25.04.8
- HPC
- Slurm
- Singularity
- Sarek 3.6.0