!! Only displaying parameters that differ from the pipeline defaults !!
-[2m--------------------------------------------------------------------------------------------------------------[0m-
If you use ViroProfiler for your analysis please cite:
The ViroProfiler pipeline
Ru, Jinlong, et al. "ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis."
Gut Microbes 15.1 (2023): 2192522. https://doi.org/10.1080/19490976.2023.2192522
The nf-core framework
Ewels, Philip A., et al. "The nf-core framework for community-curated bioinformatics pipelines."
Nature biotechnology 38.3 (2020): 276-278. https://doi.org/10.1038/s41587-020-0439-x
Software dependencies
https://github.com/deng-lab/viroprofiler/blob/main/CITATIONS.md
-[2m--------------------------------------------------------------------------------------------------------------[0m-
Aug-06 21:14:45.493 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:setup matches labels viroprofiler_base,setup for process with name VIROPROFILER:SETUP:DB_CHECKV
Aug-06 21:14:45.494 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_base matches labels viroprofiler_base,setup for process with name VIROPROFILER:SETUP:DB_CHECKV
Aug-06 21:14:45.499 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-06 21:14:45.499 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-06 21:14:45.507 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Aug-06 21:14:45.516 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=4; memory=16 GB; capacity=4; pollInterval=100ms; dumpInterval=5m
Aug-06 21:14:45.623 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:setup matches labels viroprofiler_vibrant,setup for process with name VIROPROFILER:SETUP:DB_VIBRANT
Aug-06 21:14:45.624 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_vibrant matches labels viroprofiler_vibrant,setup for process with name VIROPROFILER:SETUP:DB_VIBRANT
Aug-06 21:14:45.624 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:DB_VIBRANT matches process VIROPROFILER:SETUP:DB_VIBRANT
Aug-06 21:14:45.625 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-06 21:14:45.625 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-06 21:14:45.628 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:setup matches labels viroprofiler_virsorter2,setup for process with name VIROPROFILER:SETUP:DB_VIRSORTER2
Aug-06 21:14:45.629 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_virsorter2 matches labels viroprofiler_virsorter2,setup for process with name VIROPROFILER:SETUP:DB_VIRSORTER2
Aug-06 21:14:45.629 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:DB_VIRSORTER2 matches process VIROPROFILER:SETUP:DB_VIRSORTER2
Aug-06 21:14:45.630 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-06 21:14:45.630 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-06 21:14:45.632 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:setup matches labels viroprofiler_geneannot,setup for process with name VIROPROFILER:SETUP:DB_DRAM
Aug-06 21:14:45.633 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_geneannot matches labels viroprofiler_geneannot,setup for process with name VIROPROFILER:SETUP:DB_DRAM
Aug-06 21:14:45.633 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:DB_DRAM matches process VIROPROFILER:SETUP:DB_DRAM
Aug-06 21:14:45.634 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-06 21:14:45.634 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-06 21:14:45.636 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:setup matches labels viroprofiler_host,setup for process with name VIROPROFILER:SETUP:DB_IPHOP
Aug-06 21:14:45.636 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_host matches labels viroprofiler_host,setup for process with name VIROPROFILER:SETUP:DB_IPHOP
Aug-06 21:14:45.637 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-06 21:14:45.637 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-06 21:14:45.639 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:setup matches labels viroprofiler_base,setup for process with name VIROPROFILER:SETUP:DB_VREFSEQ
Aug-06 21:14:45.640 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_base matches labels viroprofiler_base,setup for process with name VIROPROFILER:SETUP:DB_VREFSEQ
Aug-06 21:14:45.640 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:DB_VREFSEQ matches process VIROPROFILER:SETUP:DB_VREFSEQ
Aug-06 21:14:45.641 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Aug-06 21:14:45.641 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-06 21:14:45.643 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: DB_VOGDB, GENEPRED4BIN, VIROPROFILER:SETUP:DB_DRAM, CHECKV, VIRSORTER2, DB_VIBRANT, FASTP, BBMAP_ALIGN, ABUNDANCE, MAPPING2CONTIGS2, PHAMB_RF, GENEPRED4CTG, VIBRANT, CONTIGLIB, VAMB, BRACKEN_COMBINEBRACKENOUTPUTS, DB_VIRSORTER2, DECONTAM, VIRALHOST_IPHOP, DRAMV, DB_KRAKEN2, GENEPRED, CONTIGLIB_CLUSTER, DB_VIROPROFILER, FASTQC, CHECKV4PHAMB, VRHYME, SPADES, TAXONOMY_MERGE, MULTIQC, VOGDB, DB_PHAMB, VIROPROFILER:SETUP:DB_VREFSEQ, DB_IPHOP, CHECKV4VRHYME, VIROPROFILER:SETUP:DB_VIBRANT, RESULTS_TSE, DB_MICOMPLETEDB, TAXONOMY_VCONTACT, TAXONOMY_MMSEQS, DB_CHECKV, CONTIGINDEX, MICOMPLETEDB, VIROPROFILER:SETUP:DB_VIRSORTER2, NRGENE, DB_VREFSEQ, NRPROT, EMAPPER, REPLIDEC, MAPPING2CONTIGS, BRACKEN_DB, DB_EGGNOG, DVF, BACPHLIP, VIROPROFILER:SETUP:DB_IPHOP, DB_DRAM, CUSTOM_DUMPSOFTWAREVERSIONS, VIROPROFILER:SETUP:DB_CHECKV, VIRCONTIGS_PRE, NRSEQS, ABRICATE, BRACKEN
Aug-06 21:14:45.649 [main] DEBUG nextflow.Session - Igniting dataflow network (7)
Aug-06 21:14:45.650 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:SETUP:DB_CHECKV
Aug-06 21:14:45.651 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:SETUP:DB_VIBRANT
Aug-06 21:14:45.651 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:SETUP:DB_VIRSORTER2
Aug-06 21:14:45.652 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:SETUP:DB_DRAM
Aug-06 21:14:45.652 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:SETUP:DB_IPHOP
Aug-06 21:14:45.652 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:SETUP:DB_VREFSEQ
Aug-06 21:14:45.652 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Aug-06 21:14:45.652 [main] DEBUG nextflow.Session - Session await
Aug-06 21:14:45.805 [Actor Thread 11] INFO nextflow.container.SingularityCache - Pulling Singularity image docker://denglab/viroprofiler-base:v0.2 [cache /gpfs/work5/0/gusr0570/singularity/denglab-viroprofiler-base-v0.2.img]
Aug-06 21:14:45.805 [Actor Thread 7] INFO nextflow.container.SingularityCache - Pulling Singularity image docker://denglab/viroprofiler-vibrant:v0.2 [cache /gpfs/work5/0/gusr0570/singularity/denglab-viroprofiler-vibrant-v0.2.img]
Aug-06 21:14:45.806 [Actor Thread 10] INFO nextflow.container.SingularityCache - Pulling Singularity image docker://denglab/viroprofiler-geneannot:v0.2 [cache /gpfs/work5/0/gusr0570/singularity/denglab-viroprofiler-geneannot-v0.2.img]
Aug-06 21:14:45.806 [Actor Thread 12] INFO nextflow.container.SingularityCache - Pulling Singularity image docker://denglab/viroprofiler-virsorter2:v0.2.5 [cache /gpfs/work5/0/gusr0570/singularity/denglab-viroprofiler-virsorter2-v0.2.5.img]
Aug-06 21:14:45.807 [Actor Thread 9] INFO nextflow.container.SingularityCache - Pulling Singularity image docker://denglab/viroprofiler-host:v0.1 [cache /gpfs/work5/0/gusr0570/singularity/denglab-viroprofiler-host-v0.1.img]
Aug-06 21:14:47.474 [Actor Thread 7] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=docker://denglab/viroprofiler-vibrant:v0.2 path=/gpfs/work5/0/gusr0570/singularity/denglab-viroprofiler-vibrant-v0.2.img
Aug-06 21:14:47.597 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-06 21:14:47.601 [Task submitter] INFO nextflow.Session - [e6/3a2b5b] Submitted process > VIROPROFILER:SETUP:DB_VIBRANT
Aug-06 21:14:48.480 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: VIROPROFILER:SETUP:DB_VIBRANT; status: COMPLETED; exit: 1; error: -; workDir: /gpfs/work5/0/gusr0570/work/e6/3a2b5b4f8bc4fe1b9844bd60cd24b0]
Aug-06 21:14:48.486 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=VIROPROFILER:SETUP:DB_VIBRANT; work-dir=/gpfs/work5/0/gusr0570/work/e6/3a2b5b4f8bc4fe1b9844bd60cd24b0
error [nextflow.exception.ProcessFailedException]: Process VIROPROFILER:SETUP:DB_VIBRANT terminated with an error exit status (1)
Aug-06 21:14:48.500 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'VIROPROFILER:SETUP:DB_VIBRANT'
Caused by:
Process VIROPROFILER:SETUP:DB_VIBRANT terminated with an error exit status (1)
Command executed:
if [ ! -d “/gpfs/work5/0/gusr0570/viroprofiler_db/â€/vibrant ]; then
mkdir -p “/gpfs/work5/0/gusr0570/viroprofiler_db/â€/vibrant
export VIBRANT_DATA_PATH="/opt/conda/share/vibrant-1.2.1/db"
download-db.sh “/gpfs/work5/0/gusr0570/viroprofiler_db/â€/vibrant
else
echo "VIBRANT database already exists"
fi
Command exit status:
1
Command output:
(empty)
Command error:
INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
Command 'ps' required by nextflow to collect task metrics cannot be found
Work dir:
/gpfs/work5/0/gusr0570/work/e6/3a2b5b4f8bc4fe1b9844bd60cd24b0
Description of the bug
Command 'ps' required by nextflow to collect task metrics cannot be found
Command used and terminal output
Relevant files
Aug-06 21:14:35.695 [main] DEBUG nextflow.cli.Launcher - $> nextflow run deng-lab/viroprofiler -r main -profile singularity --mode setup --db “/gpfs/work5/0/gusr0570/viroprofiler_db/†Aug-06 21:14:35.786 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.04.1 Aug-06 21:14:35.839 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/mibrahim30/.nextflow/plugins; core-plugins: nf-amazon@1.16.2,nf-azure@1.0.1,nf-codecommit@0.1.4,nf-console@1.0.5,nf-ga4gh@1.0.5,nf-google@1.7.3,nf-tower@1.5.12,nf-wave@0.8.2 Aug-06 21:14:35.858 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Aug-06 21:14:35.859 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Aug-06 21:14:35.864 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode Aug-06 21:14:35.881 [main] INFO org.pf4j.AbstractPluginManager - No plugins Aug-06 21:14:35.904 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/mibrahim30/.nextflow/scm Aug-06 21:14:37.718 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/mibrahim30/.nextflow/assets/deng-lab/viroprofiler/.git/config; branch: master; remote: origin; url: https://github.com/deng-lab/viroprofiler.git Aug-06 21:14:37.741 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] Aug-06 21:14:37.750 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/mibrahim30/.nextflow/assets/deng-lab/viroprofiler/.git/config; branch: master; remote: origin; url: https://github.com/deng-lab/viroprofiler.git Aug-06 21:14:38.796 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/mibrahim30/.nextflow/assets/deng-lab/viroprofiler/nextflow.config Aug-06 21:14:38.797 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/mibrahim30/.nextflow/assets/deng-lab/viroprofiler/nextflow.config Aug-06 21:14:38.815 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile:
singularity
Aug-06 21:14:39.919 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [standard, debug, test, apptainer, docker, shifter, charliecloud, test_denglab, conda, singularity, charliecloud_denglab, podman, slurm_denglab2] Aug-06 21:14:39.988 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion Aug-06 21:14:39.989 [main] INFO nextflow.cli.CmdRun - Launchinghttps://github.com/deng-lab/viroprofiler
[spontaneous_aryabhata] DSL2 - revision: c2a1f1871b [main] Aug-06 21:14:39.990 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Aug-06 21:14:39.990 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] Aug-06 21:14:39.994 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /home/mibrahim30/.nextflow/secrets/store.json Aug-06 21:14:39.998 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@aa752bb] - activable => nextflow.secret.LocalSecretsProvider@aa752bb Aug-06 21:14:40.070 [main] DEBUG nextflow.Session - Session UUID: c77b1232-c098-4759-b0be-8111b5210aac Aug-06 21:14:40.071 [main] DEBUG nextflow.Session - Run name: spontaneous_aryabhata Aug-06 21:14:40.071 [main] DEBUG nextflow.Session - Executor pool size: 4 Aug-06 21:14:40.088 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=12; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Aug-06 21:14:40.132 [main] DEBUG nextflow.cli.CmdRun - Version: 23.04.1 build 5866 Created: 15-04-2023 06:51 UTC (08:51 CEST) System: Linux 4.18.0-372.57.1.el8_6.x86_64 Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 20-internal-adhoc..src Encoding: UTF-8 (UTF-8) Process: 2168861@int6 [172.18.63.192] CPUs: 4 - Mem: 16 GB (15.7 GB) - Swap: 0 (0) Aug-06 21:14:40.186 [main] DEBUG nextflow.Session - Work-dir: /gpfs/work5/0/gusr0570/work [gpfs] Aug-06 21:14:40.229 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Aug-06 21:14:40.241 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Aug-06 21:14:40.416 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Aug-06 21:14:40.429 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 5; maxThreads: 1000 Aug-06 21:14:40.592 [main] DEBUG nextflow.Session - Session start Aug-06 21:14:40.598 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /gpfs/work5/0/gusr0570/output/pipeline_info/execution_trace_2023-08-06_21-14-39.txt Aug-06 21:14:40.643 [main] DEBUG nextflow.Session - Using default localLib path: /home/mibrahim30/.nextflow/assets/deng-lab/viroprofiler/lib Aug-06 21:14:40.656 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/mibrahim30/.nextflow/assets/deng-lab/viroprofiler/lib Aug-06 21:14:40.657 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/mibrahim30/.nextflow/assets/deng-lab/viroprofiler/lib/nfcore_external_java_deps.jar Aug-06 21:14:41.726 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Aug-06 21:14:41.985 [main] INFO nextflow.Nextflow --[2m--------------------------------------------------------------------------------------------------------------[0m- [0;34m [0m [0;34m oooooo oooo o8o 88 88 .o88o. o8o oooo [0m [0;34m
888. .8'
"' 88 ss 88 888"
"'888 [0m [0;34m
888. .8' oooo oooo d8b .ooooo. 8888 oooo d8b .ooooo. o888oo oooo 888 .ooooo. oooo d8b [0m [0;34m888. .8'
888888""8P d88'
88b ||888""8P d88'
88b 888888 888 d88'
88b888""8P [0m [0;34m
888.8' 888 888 888 888 || 888 888 888 888 888 888 888ooo888 888 [0m [0;34m888' 888 888 888 888 // || \\ 888 888 888 888 888 888 888 .o 888 [0m [0;34m
8' o888o d888bY8bod8P' // \\ d888b
Y8bod8P' o888o o888o o888o `Y8bod8P' d888b [0m [0;35m ViroProfiler v0.2.4[0m -[2m--------------------------------------------------------------------------------------------------------------[0m- [1mCore Nextflow options[0m [0;34mrevision : [0;32mmain[0m [0;34mrunName : [0;32mspontaneous_aryabhata[0m [0;34mcontainerEngine: [0;32msingularity[0m [0;34mlaunchDir : [0;32m/gpfs/work5/0/gusr0570[0m [0;34mworkDir : [0;32m/gpfs/work5/0/gusr0570/work[0m [0;34mprojectDir : [0;32m/home/mibrahim30/.nextflow/assets/deng-lab/viroprofiler[0m [0;34muserName : [0;32mmibrahim30[0m [0;34mprofile : [0;32msingularity[0m [0;34mconfigFiles : [0;32m/home/mibrahim30/.nextflow/assets/deng-lab/viroprofiler/nextflow.config[0m[1mInput/output options[0m [0;34mmode : [0;32msetup[0m [0;34mdb : [0;32m“/gpfs/work5/0/gusr0570/viroprofiler_db/â€[0m [0;34moutdir : [0;32moutput[0m
[1mQC[0m [0;34mcontamref_idx : [0;32m/home/mibrahim30/viroprofiler/contamination_refs/hg19/ref[0m
[1mContig library parameters[0m [0;34massemblies : [0;32mscaffolds[0m
[1mOthers[0m [0;34muse_iphop : [0;32mtrue[0m [0;34muse_dram : [0;32mtrue[0m
[1mMax job request options[0m [0;34mmax_cpus : [0;32m1[0m [0;34mmax_memory : [0;32m8.GB[0m [0;34mmax_time : [0;32m12.h[0m
!! Only displaying parameters that differ from the pipeline defaults !! -[2m--------------------------------------------------------------------------------------------------------------[0m- If you use ViroProfiler for your analysis please cite:
The ViroProfiler pipeline Ru, Jinlong, et al. "ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis." Gut Microbes 15.1 (2023): 2192522. https://doi.org/10.1080/19490976.2023.2192522
The nf-core framework Ewels, Philip A., et al. "The nf-core framework for community-curated bioinformatics pipelines." Nature biotechnology 38.3 (2020): 276-278. https://doi.org/10.1038/s41587-020-0439-x
Software dependencies https://github.com/deng-lab/viroprofiler/blob/main/CITATIONS.md -[2m--------------------------------------------------------------------------------------------------------------[0m- Aug-06 21:14:45.493 [main] DEBUG nextflow.script.ProcessConfig - Config settings
withLabel:setup
matches labelsviroprofiler_base,setup
for process with name VIROPROFILER:SETUP:DB_CHECKV Aug-06 21:14:45.494 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:viroprofiler_base
matches labelsviroprofiler_base,setup
for process with name VIROPROFILER:SETUP:DB_CHECKV Aug-06 21:14:45.499 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-06 21:14:45.499 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-06 21:14:45.507 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local Aug-06 21:14:45.516 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=4; memory=16 GB; capacity=4; pollInterval=100ms; dumpInterval=5m Aug-06 21:14:45.623 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:setup
matches labelsviroprofiler_vibrant,setup
for process with name VIROPROFILER:SETUP:DB_VIBRANT Aug-06 21:14:45.624 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:viroprofiler_vibrant
matches labelsviroprofiler_vibrant,setup
for process with name VIROPROFILER:SETUP:DB_VIBRANT Aug-06 21:14:45.624 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithName:DB_VIBRANT
matches process VIROPROFILER:SETUP:DB_VIBRANT Aug-06 21:14:45.625 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-06 21:14:45.625 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-06 21:14:45.628 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:setup
matches labelsviroprofiler_virsorter2,setup
for process with name VIROPROFILER:SETUP:DB_VIRSORTER2 Aug-06 21:14:45.629 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:viroprofiler_virsorter2
matches labelsviroprofiler_virsorter2,setup
for process with name VIROPROFILER:SETUP:DB_VIRSORTER2 Aug-06 21:14:45.629 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithName:DB_VIRSORTER2
matches process VIROPROFILER:SETUP:DB_VIRSORTER2 Aug-06 21:14:45.630 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-06 21:14:45.630 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-06 21:14:45.632 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:setup
matches labelsviroprofiler_geneannot,setup
for process with name VIROPROFILER:SETUP:DB_DRAM Aug-06 21:14:45.633 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:viroprofiler_geneannot
matches labelsviroprofiler_geneannot,setup
for process with name VIROPROFILER:SETUP:DB_DRAM Aug-06 21:14:45.633 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithName:DB_DRAM
matches process VIROPROFILER:SETUP:DB_DRAM Aug-06 21:14:45.634 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-06 21:14:45.634 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-06 21:14:45.636 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:setup
matches labelsviroprofiler_host,setup
for process with name VIROPROFILER:SETUP:DB_IPHOP Aug-06 21:14:45.636 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:viroprofiler_host
matches labelsviroprofiler_host,setup
for process with name VIROPROFILER:SETUP:DB_IPHOP Aug-06 21:14:45.637 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-06 21:14:45.637 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-06 21:14:45.639 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:setup
matches labelsviroprofiler_base,setup
for process with name VIROPROFILER:SETUP:DB_VREFSEQ Aug-06 21:14:45.640 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:viroprofiler_base
matches labelsviroprofiler_base,setup
for process with name VIROPROFILER:SETUP:DB_VREFSEQ Aug-06 21:14:45.640 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithName:DB_VREFSEQ
matches process VIROPROFILER:SETUP:DB_VREFSEQ Aug-06 21:14:45.641 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-06 21:14:45.641 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-06 21:14:45.643 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: DB_VOGDB, GENEPRED4BIN, VIROPROFILER:SETUP:DB_DRAM, CHECKV, VIRSORTER2, DB_VIBRANT, FASTP, BBMAP_ALIGN, ABUNDANCE, MAPPING2CONTIGS2, PHAMB_RF, GENEPRED4CTG, VIBRANT, CONTIGLIB, VAMB, BRACKEN_COMBINEBRACKENOUTPUTS, DB_VIRSORTER2, DECONTAM, VIRALHOST_IPHOP, DRAMV, DB_KRAKEN2, GENEPRED, CONTIGLIB_CLUSTER, DB_VIROPROFILER, FASTQC, CHECKV4PHAMB, VRHYME, SPADES, TAXONOMY_MERGE, MULTIQC, VOGDB, DB_PHAMB, VIROPROFILER:SETUP:DB_VREFSEQ, DB_IPHOP, CHECKV4VRHYME, VIROPROFILER:SETUP:DB_VIBRANT, RESULTS_TSE, DB_MICOMPLETEDB, TAXONOMY_VCONTACT, TAXONOMY_MMSEQS, DB_CHECKV, CONTIGINDEX, MICOMPLETEDB, VIROPROFILER:SETUP:DB_VIRSORTER2, NRGENE, DB_VREFSEQ, NRPROT, EMAPPER, REPLIDEC, MAPPING2CONTIGS, BRACKEN_DB, DB_EGGNOG, DVF, BACPHLIP, VIROPROFILER:SETUP:DB_IPHOP, DB_DRAM, CUSTOM_DUMPSOFTWAREVERSIONS, VIROPROFILER:SETUP:DB_CHECKV, VIRCONTIGS_PRE, NRSEQS, ABRICATE, BRACKEN Aug-06 21:14:45.649 [main] DEBUG nextflow.Session - Igniting dataflow network (7) Aug-06 21:14:45.650 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:SETUP:DB_CHECKV Aug-06 21:14:45.651 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:SETUP:DB_VIBRANT Aug-06 21:14:45.651 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:SETUP:DB_VIRSORTER2 Aug-06 21:14:45.652 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:SETUP:DB_DRAM Aug-06 21:14:45.652 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:SETUP:DB_IPHOP Aug-06 21:14:45.652 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:SETUP:DB_VREFSEQ Aug-06 21:14:45.652 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination Aug-06 21:14:45.652 [main] DEBUG nextflow.Session - Session await Aug-06 21:14:45.805 [Actor Thread 11] INFO nextflow.container.SingularityCache - Pulling Singularity image docker://denglab/viroprofiler-base:v0.2 [cache /gpfs/work5/0/gusr0570/singularity/denglab-viroprofiler-base-v0.2.img] Aug-06 21:14:45.805 [Actor Thread 7] INFO nextflow.container.SingularityCache - Pulling Singularity image docker://denglab/viroprofiler-vibrant:v0.2 [cache /gpfs/work5/0/gusr0570/singularity/denglab-viroprofiler-vibrant-v0.2.img] Aug-06 21:14:45.806 [Actor Thread 10] INFO nextflow.container.SingularityCache - Pulling Singularity image docker://denglab/viroprofiler-geneannot:v0.2 [cache /gpfs/work5/0/gusr0570/singularity/denglab-viroprofiler-geneannot-v0.2.img] Aug-06 21:14:45.806 [Actor Thread 12] INFO nextflow.container.SingularityCache - Pulling Singularity image docker://denglab/viroprofiler-virsorter2:v0.2.5 [cache /gpfs/work5/0/gusr0570/singularity/denglab-viroprofiler-virsorter2-v0.2.5.img] Aug-06 21:14:45.807 [Actor Thread 9] INFO nextflow.container.SingularityCache - Pulling Singularity image docker://denglab/viroprofiler-host:v0.1 [cache /gpfs/work5/0/gusr0570/singularity/denglab-viroprofiler-host-v0.1.img] Aug-06 21:14:47.474 [Actor Thread 7] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=docker://denglab/viroprofiler-vibrant:v0.2 path=/gpfs/work5/0/gusr0570/singularity/denglab-viroprofiler-vibrant-v0.2.img Aug-06 21:14:47.597 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Aug-06 21:14:47.601 [Task submitter] INFO nextflow.Session - [e6/3a2b5b] Submitted process > VIROPROFILER:SETUP:DB_VIBRANT Aug-06 21:14:48.480 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: VIROPROFILER:SETUP:DB_VIBRANT; status: COMPLETED; exit: 1; error: -; workDir: /gpfs/work5/0/gusr0570/work/e6/3a2b5b4f8bc4fe1b9844bd60cd24b0] Aug-06 21:14:48.486 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=VIROPROFILER:SETUP:DB_VIBRANT; work-dir=/gpfs/work5/0/gusr0570/work/e6/3a2b5b4f8bc4fe1b9844bd60cd24b0 error [nextflow.exception.ProcessFailedException]: ProcessVIROPROFILER:SETUP:DB_VIBRANT
terminated with an error exit status (1) Aug-06 21:14:48.500 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'VIROPROFILER:SETUP:DB_VIBRANT'Caused by: Process
VIROPROFILER:SETUP:DB_VIBRANT
terminated with an error exit status (1)Command executed:
if [ ! -d “/gpfs/work5/0/gusr0570/viroprofiler_db/â€/vibrant ]; then mkdir -p “/gpfs/work5/0/gusr0570/viroprofiler_db/â€/vibrant export VIBRANT_DATA_PATH="/opt/conda/share/vibrant-1.2.1/db" download-db.sh “/gpfs/work5/0/gusr0570/viroprofiler_db/â€/vibrant else echo "VIBRANT database already exists" fi
Command exit status: 1
Command output: (empty)
Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred Command 'ps' required by nextflow to collect task metrics cannot be found
Work dir: /gpfs/work5/0/gusr0570/work/e6/3a2b5b4f8bc4fe1b9844bd60cd24b0
Tip: when you have fixed the problem you can continue the execution adding the option
-resume
to the run command line Aug-06 21:14:48.516 [Task monitor] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit Aug-06 21:14:48.520 [main] DEBUG nextflow.Session - Session await > all processes finished Aug-06 21:14:48.520 [main] DEBUG nextflow.Session - Session await > all barriers passed Aug-06 21:14:48.524 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=VIROPROFILER:SETUP:DB_IPHOP; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Aug-06 21:14:48.524 [Actor Thread 2] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=VIROPROFILER:SETUP:DB_CHECKV; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Aug-06 21:14:48.524 [Actor Thread 6] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=VIROPROFILER:SETUP:DB_VREFSEQ; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Aug-06 21:14:48.524 [Actor Thread 4] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=VIROPROFILER:SETUP:DB_VIRSORTER2; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Aug-06 21:14:48.524 [Actor Thread 5] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=VIROPROFILER:SETUP:DB_DRAM; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Aug-06 21:14:48.528 [main] INFO nextflow.Nextflow - -[0;35m[ViroProfiler][0;31m Pipeline completed with errors[0m- Aug-06 21:14:48.534 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=839ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=4 GB; ] Aug-06 21:14:48.534 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Aug-06 21:14:48.535 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Aug-06 21:14:48.563 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data: [{"cpuUsage":null,"process":"DB_VIBRANT","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":839,"min":839,"q1":839,"q2":839,"q3":839,"max":839,"minLabel":"VIROPROFILER:SETUP:DB_VIBRANT","maxLabel":"VIROPROFILER:SETUP:DB_VIBRANT","q1Label":"VIROPROFILER:SETUP:DB_VIBRANT","q2Label":"VIROPROFILER:SETUP:DB_VIBRANT","q3Label":"VIROPROFILER:SETUP:DB_VIBRANT"},"writes":null}] Aug-06 21:14:49.569 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline Aug-06 21:14:49.744 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Aug-06 21:14:49.821 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) Aug-06 21:14:49.822 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- GoodbyeSystem information
Nextflow version version 23.04.1 Hadware HPC