gatk4spark/markduplicates and gatk4spark/applybqsr fail on docker_self_hosted

[GallVp]

Have you checked the docs?

• nf-core website: troubleshooting
• nf-core modules documentation

Description of the bug

Test Process GATK4SPARK_APPLYBQSR

Test [286e4c73] 'sarscov2 - bam'
> N E X T F L O W ~ version 24.04.4
> Launching /home/ubuntu/tests/286e4c730c5288bd8e27c032fc9351dc/meta/mock.nf [scruffy_cori] DSL2 - revision: 8d10e07048
> [28/7c483b] Submitted process > GATK4SPARK_APPLYBQSR (test)
> ERROR ~ Error executing process > 'GATK4SPARK_APPLYBQSR (test)'
>
> Caused by:
> Process GATK4SPARK_APPLYBQSR (test) terminated with an error exit status (126)
>
>
> Command executed:
>
> gatk
> --java-options "-Xmx4915M -XX:-UsePerfData"
> ApplyBQSRSpark
> --input test.paired_end.sorted.bam
> --output test.bam
> --reference genome.fasta
> --bqsr-recal-file test.baserecalibrator.table
>
> --spark-master local[2]
> --tmp-dir .
>
>
> cat <<-END_VERSIONS > versions.yml
> "GATK4SPARK_APPLYBQSR":
> gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.(GATK) v//; s/ .$//')
> END_VERSIONS
>
> Command exit status:
> 126
>
> Command output:
> (empty)
>
> Command error:
> Unable to find image 'quay.io/biocontainers/gatk4-spark:4.5.0.0--hdfd78af_0' locally
> 4.5.0.0--hdfd78af_0: Pulling from biocontainers/gatk4-spark
> ca7680d1025d: Pulling fs layer
> bd9ddc54bea9: Pulling fs layer
> a842ad5dfd91: Pulling fs layer
> bd9ddc54bea9: Verifying Checksum
> bd9ddc54bea9: Download complete
> ca7680d1025d: Verifying Checksum
> ca7680d1025d: Download complete
> ca7680d1025d: Pull complete
> bd9ddc54bea9: Pull complete
> a842ad5dfd91: Verifying Checksum
> a842ad5dfd91: Download complete
> a842ad5dfd91: Pull complete
> Digest: sha256:8fed31a71e7df253b90f25bf28d7e93d299b7d847c4d008f9d98117e754dcb65
> Status: Downloaded newer image for quay.io/biocontainers/gatk4-spark:4.5.0.0--hdfd78af_0
> WARNING: Your kernel does not support CPU shares or the cgroup is not mounted. Shares discarded.
> /bin/bash: .command.run: Permission denied
>
> Work dir:
> /home/ubuntu/tests/286e4c730c5288bd8e27c032fc9351dc/work/28/7c483b191a49db5b48ebc8e73f0cbf
>
> Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
>
> -- Check '/home/ubuntu/tests/286e4c730c5288bd8e27c032fc9351dc/meta/nextflow.log' file for details
> WARN: Got an interrupted exception while taking agent result | java.lang.InterruptedException
Assertion failed:

assert process.success
| |
| false
GATK4SPARK_APPLYBQSR

Command used and terminal output

No response

Relevant files

No response

System information

No response