search

icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
Other
65 stars 23 forks source link

Fail to run pipeline in SLURM #14

Closed KunFang93 closed 1 year ago

KunFang93 commented 1 year ago

Hi,

Sorry for bothering again. I found that 

nextflow run /scratch/u/kfang/Software/nextNEOpi/nextNEOpi.nf -bg --batchFile test2.csv -config conf/params.config -profile singularity -resume --accept_license --MIXCR_lic /scratch/u/kfang/Software/nextNEOpi/resources/mi.license

works in our login node of HPC cluster.

However, the pipeline failed when I tried to submit the pipeline to SLURM. The command I used:

sbatch nextflow.bash

The context in nextflow.bash

#!/usr/bin/env bash
#
#!!! This is not officially supported by 10x
#
# =============================================================================
# Job Script
# =============================================================================
#
#SBATCH -J nextNEOpi-test2
#SBATCH --export=ALL
#SBATCH --nodes=1 --ntasks-per-node=40
#SBATCH --signal=2
#SBATCH --no-requeue
#SBATCH --time=100:00:00
#SBATCH --account=vjin
#SBATCH --partition=normal
### Alternatively: --ntasks=1 --cpus-per-task={NUM_THREADS}
###   Consult with your cluster administrators to find the combination that
###   works best for single-node, multi-threaded applications on your system.
#SBATCH --mem=300G
#SBATCH -o /scratch/u/kfang/slurm_sh/%x-%j.out
#SBATCH -e /scratch/u/kfang/slurm_sh/%x-%j.err
#SBATCH --mail-user=kfang@mcw.edu ### OPTIONAL

module load nextflow
module load singularity

nextflow run /scratch/u/kfang/Software/nextNEOpi/nextNEOpi.nf --batchFile test2.csv -config conf/params.config -profile singularity -resume --accept_license --MIXCR_lic /scratch/u/kfang/Software/nextNEOpi/resources/mi.license

date

The .nextflow.log

......
Oct-24 09:27:19.138 [main] INFO  nextflow.Nextflow - -------------------------------------------------------------------------
Oct-24 09:27:19.169 [main] INFO  nextflow.script.BaseScript - WARNING: Patient353_T1star sex not specified will infer from data
Oct-24 09:27:19.176 [main] INFO  nextflow.script.BaseScript - WARNING: Patient353_T1star sex not specified will infer from data
Oct-24 09:27:19.181 [main] INFO  nextflow.script.BaseScript - WARNING: Patient353_T1star sex not specified will infer from data
Oct-24 09:27:19.330 [main] INFO  nextflow.script.BaseScript - Found /scratch/u/kfang/Software/hlahd.1.5.0/bin/hlahd.sh at: /scratch/u/kfang/Software/hlahd.1.5.0/bin/hlahd.sh
Oct-24 09:27:19.332 [main] INFO  nextflow.script.BaseScript - Found /scratch/u/kfang/Software/nextNEOpi/resources/mi.license at: /scratch/u/kfang/Software/nextNEOpi/resources/mi.license
Oct-24 09:27:19.396 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.397 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.400 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Oct-24 09:27:19.405 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=40; memory=300 GB; capacity=40; pollInterval=100ms; dumpInterval=5m
Oct-24 09:27:19.491 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name RegionsBedToIntervalList
Oct-24 09:27:19.493 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.493 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.502 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name BaitsBedToIntervalList
Oct-24 09:27:19.504 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.504 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.511 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name preprocessIntervalList
Oct-24 09:27:19.513 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.513 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.525 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name SplitIntervals
Oct-24 09:27:19.527 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.530 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.540 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name IntervalListToBed
Oct-24 09:27:19.544 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.545 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.580 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name ScatteredIntervalListToBed
Oct-24 09:27:19.582 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.582 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.594 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name FastQC
Oct-24 09:27:19.595 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FastQC` matches process FastQC
Oct-24 09:27:19.596 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.596 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.609 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name fastp
Oct-24 09:27:19.610 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:fastp` matches process fastp
Oct-24 09:27:19.611 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.611 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.620 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name FastQC_trimmed
Oct-24 09:27:19.620 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FastQC_trimmed` matches process FastQC_trimmed
Oct-24 09:27:19.622 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.622 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.639 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name make_uBAM
Oct-24 09:27:19.640 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:make_uBAM` matches process make_uBAM
Oct-24 09:27:19.640 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.640 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.649 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name Bwa
Oct-24 09:27:19.649 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:Bwa` matches process Bwa
Oct-24 09:27:19.650 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.650 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.664 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name merge_uBAM_BAM
Oct-24 09:27:19.664 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.664 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.669 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name MarkDuplicates
Oct-24 09:27:19.669 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MarkDuplicates` matches process MarkDuplicates
Oct-24 09:27:19.669 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.669 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.678 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name alignmentMetrics
Oct-24 09:27:19.678 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:alignmentMetrics` matches process alignmentMetrics
Oct-24 09:27:19.678 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.678 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.685 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name scatterBaseRecalGATK4
Oct-24 09:27:19.686 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.686 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.694 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name gatherGATK4scsatteredBQSRtables
Oct-24 09:27:19.695 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.695 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.699 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name scatterGATK4applyBQSRS
Oct-24 09:27:19.699 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:scatterGATK4applyBQSRS` matches process scatterGATK4applyBQSRS
Oct-24 09:27:19.699 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.699 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.710 [Actor Thread 37] WARN  nextflow.container.SingularityCache - Singularity cache directory has not been defined -- Remote image will be stored in the path: /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location
Oct-24 09:27:19.714 [Actor Thread 37] INFO  nextflow.container.SingularityCache - Pulling Singularity image https://apps-01.i-med.ac.at/images/singularity/nextNEOpi_1.3.2_18734d43.sif [cache /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/singularity/apps-01.i-med.ac.at-images-singularity-nextNEOpi_1.3.2_18734d43.sif]
Oct-24 09:27:19.719 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name GatherRecalBamFiles
Oct-24 09:27:19.719 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GatherRecalBamFiles` matches process GatherRecalBamFiles
Oct-24 09:27:19.719 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.719 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.723 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name GetPileup
Oct-24 09:27:19.723 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.723 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.728 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:GATK3` matches labels `GATK3` for process with name install_conda_GATK3
Oct-24 09:27:19.729 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.729 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.736 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name Mutect2
Oct-24 09:27:19.736 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:Mutect2` matches process Mutect2
Oct-24 09:27:19.737 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.737 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.741 [Actor Thread 30] INFO  nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/gatk:3.8--hdfd78af_11 [cache /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/singularity/depot.galaxyproject.org-singularity-gatk-3.8--hdfd78af_11.img]
Oct-24 09:27:19.742 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name gatherMutect2VCFs
Oct-24 09:27:19.742 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.742 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.748 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name FilterMutect2
Oct-24 09:27:19.749 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.749 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.753 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name HaploTypeCaller
Oct-24 09:27:19.754 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:HaploTypeCaller` matches process HaploTypeCaller
Oct-24 09:27:19.754 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.754 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.757 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name CNNScoreVariants
Oct-24 09:27:19.757 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CNNScoreVariants` matches process CNNScoreVariants
Oct-24 09:27:19.758 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.758 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.761 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name MergeHaploTypeCallerGermlineVCF
Oct-24 09:27:19.761 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.761 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.764 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name FilterGermlineVariantTranches
Oct-24 09:27:19.765 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.765 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.771 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:GATK3` matches labels `GATK3` for process with name IndelRealignerIntervals
Oct-24 09:27:19.771 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:IndelRealignerIntervals` matches process IndelRealignerIntervals
Oct-24 09:27:19.771 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.771 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.772 [main] DEBUG nextflow.processor.TaskProcessor - Creating *combiner* operator for each param(s) at index(es): [4]
Oct-24 09:27:19.779 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name GatherRealignedBamFiles
Oct-24 09:27:19.779 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GatherRealignedBamFiles` matches process GatherRealignedBamFiles
Oct-24 09:27:19.780 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.780 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.786 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name VarscanSomaticScattered
Oct-24 09:27:19.786 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VarscanSomaticScattered` matches process VarscanSomaticScattered
Oct-24 09:27:19.787 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.787 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.791 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name gatherVarscanVCFs
Oct-24 09:27:19.792 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.792 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.797 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name ProcessVarscan
Oct-24 09:27:19.797 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.797 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.802 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name FilterVarscan
Oct-24 09:27:19.803 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.803 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.805 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name MergeAndRenameSamplesInVarscanVCF
Oct-24 09:27:19.806 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.806 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.807 [main] INFO  nextflow.Nextflow - INFO: Mutect1 not available, skipping....
Oct-24 09:27:19.812 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:Manta` matches labels `Manta` for process with name MantaSomaticIndels
Oct-24 09:27:19.812 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MantaSomaticIndels` matches process MantaSomaticIndels
Oct-24 09:27:19.812 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.812 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.817 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:Strelka` matches labels `Strelka` for process with name StrelkaSomatic
Oct-24 09:27:19.817 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:StrelkaSomatic` matches process StrelkaSomatic
Oct-24 09:27:19.818 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.818 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.821 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name finalizeStrelkaVCF
Oct-24 09:27:19.821 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.821 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.828 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name mkHCsomaticVCF
Oct-24 09:27:19.829 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.829 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.846 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:VEP` matches labels `VEP` for process with name VepTab
Oct-24 09:27:19.847 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.847 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.850 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name mkCombinedVCF
Oct-24 09:27:19.850 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:mkCombinedVCF` matches process mkCombinedVCF
Oct-24 09:27:19.850 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.850 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.857 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:VEP` matches labels `VEP` for process with name VEPvcf
Oct-24 09:27:19.858 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.858 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.863 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:GATK3` matches labels `GATK3` for process with name ReadBackedphasing
Oct-24 09:27:19.863 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:ReadBackedphasing` matches process ReadBackedphasing
Oct-24 09:27:19.863 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.863 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.865 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:AlleleCounter` matches labels `AlleleCounter` for process with name AlleleCounter
Oct-24 09:27:19.866 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.866 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.871 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name ConvertAlleleCounts
Oct-24 09:27:19.871 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.871 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.874 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name Ascat
Oct-24 09:27:19.874 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.874 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.882 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name SequenzaUtils
Oct-24 09:27:19.882 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SequenzaUtils` matches process SequenzaUtils
Oct-24 09:27:19.883 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.883 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.883 [main] DEBUG nextflow.processor.TaskProcessor - Creating *combiner* operator for each param(s) at index(es): [1]
Oct-24 09:27:19.886 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name gatherSequenzaInput
Oct-24 09:27:19.886 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:gatherSequenzaInput` matches process gatherSequenzaInput
Oct-24 09:27:19.887 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.887 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.889 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name Sequenza
Oct-24 09:27:19.890 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.890 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.896 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:CNVkit` matches labels `CNVkit` for process with name make_CNVkit_access_file
Oct-24 09:27:19.896 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.896 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.899 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:CNVkit` matches labels `CNVkit` for process with name CNVkit
Oct-24 09:27:19.899 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CNVkit` matches process CNVkit
Oct-24 09:27:19.900 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.900 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.905 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name Clonality
Oct-24 09:27:19.906 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.906 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.910 [Actor Thread 26] INFO  nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0 [cache /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/singularity/depot.galaxyproject.org-singularity-cnvkit-0.9.9--pyhdfd78af_0.img]
Oct-24 09:27:19.911 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name MutationalBurden
Oct-24 09:27:19.911 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MutationalBurden` matches process MutationalBurden
Oct-24 09:27:19.911 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.912 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.916 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name MutationalBurdenCoding
Oct-24 09:27:19.916 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MutationalBurdenCoding` matches process MutationalBurdenCoding
Oct-24 09:27:19.916 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.916 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.919 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name mhc_extract
Oct-24 09:27:19.919 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:mhc_extract` matches process mhc_extract
Oct-24 09:27:19.919 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.919 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.922 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name pre_map_hla
Oct-24 09:27:19.923 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:pre_map_hla` matches process pre_map_hla
Oct-24 09:27:19.923 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.923 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.925 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name OptiType
Oct-24 09:27:19.926 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.926 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.929 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name pre_map_hla_RNA
Oct-24 09:27:19.929 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:pre_map_hla_RNA` matches process pre_map_hla_RNA
Oct-24 09:27:19.929 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.929 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.932 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name OptiType_RNA
Oct-24 09:27:19.932 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.932 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.936 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:HLAHD` matches labels `HLAHD` for process with name run_hla_hd
Oct-24 09:27:19.936 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:run_hla_hd` matches process run_hla_hd
Oct-24 09:27:19.936 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.936 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.948 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name get_vhla
Oct-24 09:27:19.949 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.949 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.959 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:Neofuse` matches process Neofuse
Oct-24 09:27:19.959 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.959 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.963 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.963 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.966 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name add_geneID
Oct-24 09:27:19.967 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.967 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.973 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pVACtools` matches labels `pVACtools` for process with name gene_annotator
Oct-24 09:27:19.974 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.974 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.988 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pVACtools` matches labels `pVACtools` for process with name pVACseq
Oct-24 09:27:19.988 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:pVACseq` matches process pVACseq
Oct-24 09:27:19.988 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.988 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:19.993 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:19.994 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:20.003 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pVACtools` matches labels `pVACtools` for process with name aggregated_reports
Oct-24 09:27:20.003 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:20.003 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:20.013 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pVACtools` matches labels `pVACtools` for process with name pVACtools_generate_protein_seq
Oct-24 09:27:20.014 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:20.014 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:20.024 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name pepare_mixMHC2_seq
Oct-24 09:27:20.025 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:20.025 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:20.028 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:20.028 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:20.034 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name mixMHC2pred
Oct-24 09:27:20.035 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:20.035 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:20.041 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name addCCF
Oct-24 09:27:20.043 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:20.043 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:20.057 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name make_epitopes_fasta
Oct-24 09:27:20.057 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:20.057 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:20.062 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:Blast` matches labels `Blast` for process with name blast_epitopes
Oct-24 09:27:20.062 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:blast_epitopes` matches process blast_epitopes
Oct-24 09:27:20.063 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:20.063 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:20.069 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name add_blast_hits
Oct-24 09:27:20.069 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:20.069 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:20.075 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name csin
Oct-24 09:27:20.075 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:20.075 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:20.076 [Actor Thread 27] DEBUG nextflow.util.CacheHelper - Unable to get file attributes file: /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/.mixmhc2pred_install_ok.chck -- Cause: java.nio.file.NoSuchFileException: /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/.mixmhc2pred_install_ok.chck
Oct-24 09:27:20.077 [Actor Thread 27] DEBUG nextflow.util.CacheHelper - Unable to get file attributes file: /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/MixMHC2pred -- Cause: java.nio.file.NoSuchFileException: /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/MixMHC2pred
Oct-24 09:27:20.082 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:20.082 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:20.088 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:IGS` matches labels `IGS` for process with name immunogenicity_scoring
Oct-24 09:27:20.089 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:20.089 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:20.098 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:mixcr` matches process mixcr
Oct-24 09:27:20.099 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:20.099 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:20.107 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name collectSampleInfo
Oct-24 09:27:20.107 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:20.107 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:20.114 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Unable to get file attributes file: /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/.igs_install_ok.chck -- Cause: java.nio.file.NoSuchFileException: /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/.igs_install_ok.chck
Oct-24 09:27:20.114 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Unable to get file attributes file: /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/IGS -- Cause: java.nio.file.NoSuchFileException: /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/IGS
Oct-24 09:27:20.116 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextNEOpiENV` matches labels `nextNEOpiENV` for process with name multiQC
Oct-24 09:27:20.116 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-24 09:27:20.116 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-24 09:27:20.118 [main] DEBUG nextflow.Session - Workflow process names [dsl1]: link_IGS, mhc_extract, mkHCsomaticVCF, AlleleCounter, run_hla_hd, link_mixcr, Neofuse, GatherRecalBamFiles, add_blast_hits, check_PE, merge_uBAM_BAM, gatherSequenzaInput, concat_pVACseq_files, get_vhla, collectSampleInfo, StrelkaSomatic, add_geneID, gatherGATK4scsatteredBQSRtables, install_mixMHC2pred, pVACtools_generate_protein_seq, pepare_mixMHC2_seq, link_mixMHC2pred, ControlFREECviz, FilterMutect2, installVEPplugins, finalizeStrelkaVCF, SequenzaUtils, install_mixcr, fastp, mkCombinedVCF, CNVkit, IntervalListToBed, gene_annotator, make_uBAM, Mutect2, BaitsBedToIntervalList, ReadBackedphasing, IndelRealignerIntervals, Mpileup4ControFREEC, gatherVarscanVCFs, FilterVarscan, gatherMutect2VCFs, GetPileup, Clonality, scatterBaseRecalGATK4, install_IEDB, MantaSomaticIndels, OptiType, VarscanSomaticScattered, VEPvcf, Bwa, ProcessVarscan, Ascat, FastQC, addCCF, publish_NeoFuse, MutationalBurden, make_epitopes_fasta, scatterGATK4applyBQSRS, bam2fastq, install_IGS, OptiType_RNA, ControlFREEC, gatherMpileups, ScatteredIntervalListToBed, alignmentMetrics, aggregated_reports, CNNScoreVariants, FilterGermlineVariantTranches, csin, RegionsBedToIntervalList, preprocessIntervalList, installVEPcache, SplitIntervals, GatherRealignedBamFiles, MutationalBurdenCoding, pre_map_hla_RNA, VepTab, MarkDuplicates, multiQC, immunogenicity_scoring, merge_fastq, ConvertAlleleCounts, MergeHaploTypeCallerGermlineVCF, pre_map_hla, HaploTypeCaller, Sequenza, run_hla_hd_RNA, MergeAndRenameSamplesInVarscanVCF, make_CNVkit_access_file, blast_epitopes, install_conda_GATK3, pVACseq, mixcr, Mutect1scattered, FastQC_trimmed, gatherMutect1VCFs, mixMHC2pred
Oct-24 09:27:20.122 [main] DEBUG nextflow.script.ScriptRunner - > Await termination 
Oct-24 09:27:20.122 [main] DEBUG nextflow.Session - Session await
Oct-24 09:27:20.167 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-24 09:27:20.174 [Task submitter] INFO  nextflow.Session - [55/52f40d] Submitted process > install_mixMHC2pred (install mixMHC2pred)
Oct-24 09:27:20.194 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-24 09:27:20.195 [Task submitter] INFO  nextflow.Session - [d3/f339e4] Submitted process > install_IGS (install IGS)
Oct-24 09:27:21.355 [Actor Thread 30] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/gatk:3.8--hdfd78af_11 path=/scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/singularity/depot.galaxyproject.org-singularity-gatk-3.8--hdfd78af_11.img
Oct-24 09:27:21.470 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-24 09:27:21.470 [Task submitter] INFO  nextflow.Session - [53/441b16] Submitted process > install_conda_GATK3 (install GATK3)
Oct-24 09:27:21.527 [Actor Thread 26] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0 path=/scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/singularity/depot.galaxyproject.org-singularity-cnvkit-0.9.9--pyhdfd78af_0.img
Oct-24 09:27:21.558 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-24 09:27:21.559 [Task submitter] INFO  nextflow.Session - [a0/476d14] Submitted process > make_CNVkit_access_file (mkCNVkitaccess)
Oct-24 09:27:22.008 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: install_IGS (install IGS); status: COMPLETED; exit: 127; error: -; workDir: /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/d3/f339e46faa15594316aff49b0ce08b]
Oct-24 09:27:22.038 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'install_IGS (install IGS)'

Caused by:
  Process `install_IGS (install IGS)` terminated with an error exit status (127)

Command executed:

  mkdir -p /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/IGS && \
  curl -sLk https://github.com/vincentlaboratories/neoag/raw/master/NeoAg_immunogenicity_predicition_GBM.R -o /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/IGS/NeoAg_immunogenicity_predicition_GBM.R && \
  curl -sLk https://github.com/vincentlaboratories/neoag/raw/master/Final_gbm_model.rds -o /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/IGS/Final_gbm_model.rds && \
  patch -p0 /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/IGS/NeoAg_immunogenicity_predicition_GBM.R /scratch/u/kfang/Software/nextNEOpi/assets/NeoAg_immunogenicity_predicition_GBM.patch && \
  chmod +x /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/IGS/NeoAg_immunogenicity_predicition_GBM.R  && \
  echo "OK" > .igs_install_ok.chck && \
  cp -f .igs_install_ok.chck /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/.igs_install_ok.chck

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 5: patch: command not found

Work dir:
  /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/d3/f339e46faa15594316aff49b0ce08b

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Oct-24 09:27:22.069 [Task monitor] INFO  nextflow.Session - Execution cancelled -- Finishing pending tasks before exit
Oct-24 09:27:22.092 [main] DEBUG nextflow.Session - Session await > all process finished
Oct-24 09:27:22.122 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: install_conda_GATK3 (install GATK3); status: COMPLETED; exit: 0; error: -; workDir: /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/53/441b16ba5977950d5448d7a6e1f911]
Oct-24 09:27:22.163 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: install_mixMHC2pred (install mixMHC2pred); status: COMPLETED; exit: 0; error: -; workDir: /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/55/52f40d58eae2a4469f0bb28f90f70a]
Oct-24 09:27:24.356 [Actor Thread 37] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://apps-01.i-med.ac.at/images/singularity/nextNEOpi_1.3.2_18734d43.sif path=/scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/singularity/apps-01.i-med.ac.at-images-singularity-nextNEOpi_1.3.2_18734d43.sif
Oct-24 09:27:45.317 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: make_CNVkit_access_file (mkCNVkitaccess); status: COMPLETED; exit: 0; error: -; workDir: /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/work/a0/476d141585af12e09203e1cb8cd556]
Oct-24 09:27:45.344 [main] DEBUG nextflow.Session - Session await > all barriers passed
Oct-24 09:27:45.438 [main] INFO  nextflow.Nextflow - [icbi/nextNEOpi] Pipeline Complete! You can find your results in /scratch/u/kfang/ChenHZ_lab/Neoantigen/test2/RESULTS
Oct-24 09:27:45.442 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=3; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=8; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=24.6s; failedDuration=1.8s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=4; peakCpus=4; peakMemory=0; ]
Oct-24 09:27:45.442 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file
Oct-24 09:27:45.446 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report
Oct-24 09:27:45.579 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
  [{"cpuUsage":null,"process":"install_IGS","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":1769,"min":1769,"q1":1769,"q2":1769,"q3":1769,"max":1769,"minLabel":"install_IGS (install IGS)","maxLabel":"install_IGS (install IGS)","q1Label":"install_IGS (install IGS)","q2Label":"install_IGS (install IGS)","q3Label":"install_IGS (install IGS)"},"writes":null},{"cpuUsage":{"mean":143.7,"min":143.7,"q1":143.7,"q2":143.7,"q3":143.7,"max":143.7,"minLabel":"install_conda_GATK3 (install GATK3)","maxLabel":"install_conda_GATK3 (install GATK3)","q1Label":"install_conda_GATK3 (install GATK3)","q2Label":"install_conda_GATK3 (install GATK3)","q3Label":"install_conda_GATK3 (install GATK3)"},"process":"install_conda_GATK3","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":{"mean":66182,"min":66182,"q1":66182,"q2":66182,"q3":66182,"max":66182,"minLabel":"install_conda_GATK3 (install GATK3)","maxLabel":"install_conda_GATK3 (install GATK3)","q1Label":"install_conda_GATK3 (install GATK3)","q2Label":"install_conda_GATK3 (install GATK3)","q3Label":"install_conda_GATK3 (install GATK3)"},"cpu":{"mean":143.7,"min":143.7,"q1":143.7,"q2":143.7,"q3":143.7,"max":143.7,"minLabel":"install_conda_GATK3 (install GATK3)","maxLabel":"install_conda_GATK3 (install GATK3)","q1Label":"install_conda_GATK3 (install GATK3)","q2Label":"install_conda_GATK3 (install GATK3)","q3Label":"install_conda_GATK3 (install GATK3)"},"time":null,"writes":{"mean":227,"min":227,"q1":227,"q2":227,"q3":227,"max":227,"minLabel":"install_conda_GATK3 (install GATK3)","maxLabel":"install_conda_GATK3 (install GATK3)","q1Label":"install_conda_GATK3 (install GATK3)","q2Label":"install_conda_GATK3 (install GATK3)","q3Label":"install_conda_GATK3 (install GATK3)"}},{"cpuUsage":{"mean":19.3,"min":19.3,"q1":19.3,"q2":19.3,"q3":19.3,"max":19.3,"minLabel":"install_mixMHC2pred (install mixMHC2pred)","maxLabel":"install_mixMHC2pred (install mixMHC2pred)","q1Label":"install_mixMHC2pred (install mixMHC2pred)","q2Label":"install_mixMHC2pred (install mixMHC2pred)","q3Label":"install_mixMHC2pred (install mixMHC2pred)"},"process":"install_mixMHC2pred","mem":{"mean":1634304,"min":1634304,"q1":1634304,"q2":1634304,"q3":1634304,"max":1634304,"minLabel":"install_mixMHC2pred (install mixMHC2pred)","maxLabel":"install_mixMHC2pred (install mixMHC2pred)","q1Label":"install_mixMHC2pred (install mixMHC2pred)","q2Label":"install_mixMHC2pred (install mixMHC2pred)","q3Label":"install_mixMHC2pred (install mixMHC2pred)"},"memUsage":null,"timeUsage":null,"vmem":{"mean":116150272,"min":116150272,"q1":116150272,"q2":116150272,"q3":116150272,"max":116150272,"minLabel":"install_mixMHC2pred (install mixMHC2pred)","maxLabel":"install_mixMHC2pred (install mixMHC2pred)","q1Label":"install_mixMHC2pred (install mixMHC2pred)","q2Label":"install_mixMHC2pred (install mixMHC2pred)","q3Label":"install_mixMHC2pred (install mixMHC2pred)"},"reads":{"mean":10027852,"min":10027852,"q1":10027852,"q2":10027852,"q3":10027852,"max":10027852,"minLabel":"install_mixMHC2pred (install mixMHC2pred)","maxLabel":"install_mixMHC2pred (install mixMHC2pred)","q1Label":"install_mixMHC2pred (install mixMHC2pred)","q2Label":"install_mixMHC2pred (install mixMHC2pred)","q3Label":"install_mixMHC2pred (install mixMHC2pred)"},"cpu":{"mean":19.3,"min":19.3,"q1":19.3,"q2":19.3,"q3":19.3,"max":19.3,"minLabel":"install_mixMHC2pred (install mixMHC2pred)","maxLabel":"install_mixMHC2pred (install mixMHC2pred)","q1Label":"install_mixMHC2pred (install mixMHC2pred)","q2Label":"install_mixMHC2pred (install mixMHC2pred)","q3Label":"install_mixMHC2pred (install mixMHC2pred)"},"time":{"mean":1620,"min":1620,"q1":1620,"q2":1620,"q3":1620,"max":1620,"minLabel":"install_mixMHC2pred (install mixMHC2pred)","maxLabel":"install_mixMHC2pred (install mixMHC2pred)","q1Label":"install_mixMHC2pred (install mixMHC2pred)","q2Label":"install_mixMHC2pred (install mixMHC2pred)","q3Label":"install_mixMHC2pred (install mixMHC2pred)"},"writes":{"mean":15253171,"min":15253171,"q1":15253171,"q2":15253171,"q3":15253171,"max":15253171,"minLabel":"install_mixMHC2pred (install mixMHC2pred)","maxLabel":"install_mixMHC2pred (install mixMHC2pred)","q1Label":"install_mixMHC2pred (install mixMHC2pred)","q2Label":"install_mixMHC2pred (install mixMHC2pred)","q3Label":"install_mixMHC2pred (install mixMHC2pred)"}},{"cpuUsage":{"mean":111.4,"min":111.4,"q1":111.4,"q2":111.4,"q3":111.4,"max":111.4,"minLabel":"make_CNVkit_access_file (mkCNVkitaccess)","maxLabel":"make_CNVkit_access_file (mkCNVkitaccess)","q1Label":"make_CNVkit_access_file (mkCNVkitaccess)","q2Label":"make_CNVkit_access_file (mkCNVkitaccess)","q3Label":"make_CNVkit_access_file (mkCNVkitaccess)"},"process":"make_CNVkit_access_file","mem":{"mean":119500800,"min":119500800,"q1":119500800,"q2":119500800,"q3":119500800,"max":119500800,"minLabel":"make_CNVkit_access_file (mkCNVkitaccess)","maxLabel":"make_CNVkit_access_file (mkCNVkitaccess)","q1Label":"make_CNVkit_access_file (mkCNVkitaccess)","q2Label":"make_CNVkit_access_file (mkCNVkitaccess)","q3Label":"make_CNVkit_access_file (mkCNVkitaccess)"},"memUsage":null,"timeUsage":null,"vmem":{"mean":5785579520,"min":5785579520,"q1":5785579520,"q2":5785579520,"q3":5785579520,"max":5785579520,"minLabel":"make_CNVkit_access_file (mkCNVkitaccess)","maxLabel":"make_CNVkit_access_file (mkCNVkitaccess)","q1Label":"make_CNVkit_access_file (mkCNVkitaccess)","q2Label":"make_CNVkit_access_file (mkCNVkitaccess)","q3Label":"make_CNVkit_access_file (mkCNVkitaccess)"},"reads":{"mean":3203800228,"min":3203800228,"q1":3203800228,"q2":3203800228,"q3":3203800228,"max":3203800228,"minLabel":"make_CNVkit_access_file (mkCNVkitaccess)","maxLabel":"make_CNVkit_access_file (mkCNVkitaccess)","q1Label":"make_CNVkit_access_file (mkCNVkitaccess)","q2Label":"make_CNVkit_access_file (mkCNVkitaccess)","q3Label":"make_CNVkit_access_file (mkCNVkitaccess)"},"cpu":{"mean":111.4,"min":111.4,"q1":111.4,"q2":111.4,"q3":111.4,"max":111.4,"minLabel":"make_CNVkit_access_file (mkCNVkitaccess)","maxLabel":"make_CNVkit_access_file (mkCNVkitaccess)","q1Label":"make_CNVkit_access_file (mkCNVkitaccess)","q2Label":"make_CNVkit_access_file (mkCNVkitaccess)","q3Label":"make_CNVkit_access_file (mkCNVkitaccess)"},"time":{"mean":23000,"min":23000,"q1":23000,"q2":23000,"q3":23000,"max":23000,"minLabel":"make_CNVkit_access_file (mkCNVkitaccess)","maxLabel":"make_CNVkit_access_file (mkCNVkitaccess)","q1Label":"make_CNVkit_access_file (mkCNVkitaccess)","q2Label":"make_CNVkit_access_file (mkCNVkitaccess)","q3Label":"make_CNVkit_access_file (mkCNVkitaccess)"},"writes":{"mean":450430,"min":450430,"q1":450430,"q2":450430,"q3":450430,"max":450430,"minLabel":"make_CNVkit_access_file (mkCNVkitaccess)","maxLabel":"make_CNVkit_access_file (mkCNVkitaccess)","q1Label":"make_CNVkit_access_file (mkCNVkitaccess)","q2Label":"make_CNVkit_access_file (mkCNVkitaccess)","q3Label":"make_CNVkit_access_file (mkCNVkitaccess)"}}]
Oct-24 09:27:46.062 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline
Oct-24 09:27:46.209 [main] WARN  nextflow.dag.GraphvizRenderer - To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Oct-24 09:27:46.357 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Oct-24 09:27:46.413 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

I notice that there is option that to use -profile cluster in the pipeline but I am not sure how to use it for our SLURM system. I wondered if you could give any suggestions of running the pipeline in SLURM. Thanks for your time and help!

Best, Kun

riederd commented 1 year ago

Hi, I guess you need to install the "patch" program on your system.

KunFang93 commented 1 year ago

Hi,

If I am understand correctly, we only need to install singularity and nextflow and the pipeline will take care of all other packages installation? I wondered how could we install the "patch" program and why this 'patch' program are not included in the pipeline? Thanks~

Best, Kun

riederd commented 1 year ago

It seems we overlooked that in the documentation, because of patch was installed per default on our system. I put it on the todos for the next release.

KunFang93 commented 1 year ago

Got it, thanks for your help!