docker: Error response from daemon: failed to create endpoint nxf-KT6fcPSRKcRvNRrVSGzfy0iU on network bridge

[tyamaguchi-ucla]

Describe the issue
A clear and concise description of what the issue is. Please include the following in your issue report along with any explicit errors observed

• Pipeline release version /hot/software/pipeline/metapipeline-DNA/Nextflow/release/6.0.0-rc.2/main.nf
• Cluster you are using - Slurm AL (We need to update this template to add the new prod cluster)
• Node type F72_3TB
• Submission method (submission script) /hot/data/unregistered/Luo-Yamaguchi-PRAD-SHCV/pipeline-input/submit_metapipeline-DNA-LYPRSHCV000001.sh
• Actual submission script (python submission script, "nextflow run ...", etc.)
  /hot/data/unregistered/Luo-Yamaguchi-PRAD-SHCV/pipeline-input/submit_metapipeline-DNA-LYPRSHCV000001.sh
• Sbatch or qsub command and logs if applicable
  /hot/data/unregistered/Luo-Yamaguchi-PRAD-SHCV/pipeline-input/LYPRSHCV_metapipeline-DNA-LYPRSHCV000001-BAM.log
• Config files /hot/data/unregistered/Luo-Yamaguchi-PRAD-SHCV/pipeline-input/LYPRSHCV_DNA-metapipeline-LYPRSHCV000001.config
• Path to the working directory
• Any logs produced by the pipeline
  /hot/data/unregistered/Luo-Yamaguchi-PRAD-SHCV/metapipeline-DNA-6.0.0-rc.2/LYPRSHCV/log-metapipeline-DNA-20240421T011425Z
/hot/data/unregistered/Luo-Yamaguchi-PRAD-SHCV/leading-LYPRSHCV000001/d5/8938a931932889dae3ebcb3897211d/.nextflow.log
  To Reproduce
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Expected behavior
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Screenshots
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Additional context

  ERROR ~ Error executing process > 'run_HaplotypeCallerGVCF_GATK (54)'

  Caused by:
    Process `run_HaplotypeCallerGVCF_GATK (54)` terminated with an error exit status (125)

  Command executed:

    set -euo pipefail

    gatk --java-options "-Xmx7168m -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -Djava.io.tmpdir=/scratch/150115/work-call-gSNP-LYPRSHCV000001"         HaplotypeCaller
      --input BWA-MEM2-2.2.1_GATK-4.2.4.1_LYPRSHCV_LYPRSHCV000001-T002-P02-F.bam         --output GATK-4.2.4.1_LYPRSHCV_LYPRSHCV000001-T002-P02-F_0017-raw-variants.g.
vcf.gz         --reference Homo_sapiens_assembly38.fasta         --verbosity INFO         --output-mode EMIT_VARIANTS_ONLY         --emit-ref-confidence GVCF
--dbsnp resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz         --sample-ploidy 2         --intervals 0017-contig.interval_list

  Command exit status:
    125

  Command output:
    (empty)

  Command error:
    docker: Error response from daemon: failed to create endpoint nxf-KT6fcPSRKcRvNRrVSGzfy0iU on network bridge: failed to add the host (vetheb05268) <=> sandbox (ve
the90fc11) pair interfaces: cannot allocate memory.
    time="2024-04-25T22:08:34-07:00" level=error msg="error waiting for container: context canceled"

  Work dir:
    /scratch/150115/work-call-gSNP-LYPRSHCV000001/ff/116cc5f642812b9966c5e4edd128a8