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nextflow.log
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Jan-19 08:48:37.915 [main] DEBUG nextflow.cli.Launcher - Setting HTTP proxy: [httpproxy.zit.med.uni-tuebingen.de, 88]
Jan-19 08:48:37.978 [main] DEBUG nextflow.cli.Launcher - Setting HTTPS proxy: [httpproxy.zit.med.uni-tuebingen.de, 88]
Jan-19 08:48:37.978 [main] DEBUG nextflow.cli.Launcher - Setting http proxy: [httpproxy.zit.med.uni-tuebingen.de, 88]
Jan-19 08:48:37.978 [main] DEBUG nextflow.cli.Launcher - Setting https proxy: [httpproxy.zit.med.uni-tuebingen.de, 88]
Jan-19 08:48:37.978 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/bacass -r 2.0.0 --input samplesheet-bacass.csv --kraken2db /home/sysgen/db/kraken/k2_pluspf_16gb_20210127.tar --annotation_tool dfast --assembly_type hybrid -profile docker --outdir results
Jan-19 08:48:38.032 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 21.04.1
Jan-19 08:48:39.684 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/sysgen/.nextflow/assets/nf-core/bacass/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/bacass.git
Jan-19 08:48:39.711 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/sysgen/.nextflow/assets/nf-core/bacass/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/bacass.git
Jan-19 08:48:40.197 [main] INFO nextflow.cli.CmdRun - Launching `nf-core/bacass` [gigantic_banach] - revision: 959967364c [2.0.0]
Jan-19 08:48:40.956 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/sysgen/.nextflow/assets/nf-core/bacass/nextflow.config
Jan-19 08:48:40.959 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/sysgen/.nextflow/assets/nf-core/bacass/nextflow.config
Jan-19 08:48:40.981 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Jan-19 08:48:41.523 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jan-19 08:48:41.524 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jan-19 08:48:41.529 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Jan-19 08:48:41.625 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [debug, test, test_long_miniasm, test_hybrid, test_long, docker, shifter, charliecloud, conda, singularity, test_dfast, test_full, podman]
Jan-19 08:48:41.670 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/sysgen/.nextflow/plugins
Jan-19 08:48:41.672 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jan-19 08:48:41.673 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins local root: .nextflow/plr/empty
Jan-19 08:48:41.680 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jan-19 08:48:41.681 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jan-19 08:48:41.683 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Jan-19 08:48:41.699 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Jan-19 08:48:41.785 [main] DEBUG nextflow.Session - Session uuid: e402140f-4fc8-4e5e-af36-e1d282ab4844
Jan-19 08:48:41.785 [main] DEBUG nextflow.Session - Run name: gigantic_banach
Jan-19 08:48:41.786 [main] DEBUG nextflow.Session - Executor pool size: 112
Jan-19 08:48:41.835 [main] DEBUG nextflow.cli.CmdRun -
Version: 21.04.1 build 5556
Created: 14-05-2021 15:20 UTC (17:20 CEST)
System: Linux 4.15.0-163-generic
Runtime: Groovy 3.0.7 on OpenJDK 64-Bit Server VM 11.0.8-internal+0-adhoc..src
Encoding: UTF-8 (UTF-8)
Process: 16991@supermicro02 [10.24.11.83]
CPUs: 112 - Mem: 1006.6 GB (25.7 GB) - Swap: 14.9 GB (9.8 GB)
Jan-19 08:48:41.874 [main] DEBUG nextflow.Session - Work-dir: /home/sysgen/Desktop/ncct-projects/2201-Kostner-Assembly/work [xfs]
Jan-19 08:48:41.908 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jan-19 08:48:41.928 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jan-19 08:48:42.254 [main] DEBUG nextflow.Session - Session start invoked
Jan-19 08:48:42.262 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/sysgen/Desktop/ncct-projects/2201-Kostner-Assembly/results/pipeline_info/execution_trace_2022-01-19_08-48-41.txt
Jan-19 08:48:42.288 [main] DEBUG nextflow.Session - Using default localLib path: /home/sysgen/.nextflow/assets/nf-core/bacass/lib
Jan-19 08:48:42.296 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/sysgen/.nextflow/assets/nf-core/bacass/lib
Jan-19 08:48:42.298 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/sysgen/.nextflow/assets/nf-core/bacass/lib/nfcore_external_java_deps.jar
Jan-19 08:48:43.803 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jan-19 08:48:44.103 [main] INFO nextflow.Nextflow -
-[2m----------------------------------------------------[0m-
[0;32m,--.[0;30m/[0;32m,-.[0m
[0;34m ___ __ __ __ ___ [0;32m/,-._.--~'[0m
[0;34m |\ | |__ __ / ` / \ |__) |__ [0;33m} {[0m
[0;34m | \| | \__, \__/ | \ |___ [0;32m\`-._,-`-,[0m
[0;32m`._,._,'[0m
[0;35m nf-core/bacass v2.0.0[0m
-[2m----------------------------------------------------[0m-
[1mCore Nextflow options[0m
[0;34mrevision : [0;32m2.0.0[0m
[0;34mrunName : [0;32mgigantic_banach[0m
[0;34mcontainerEngine: [0;32mdocker[0m
[0;34mlaunchDir : [0;32m/home/sysgen/Desktop/ncct-projects/2201-Kostner-Assembly[0m
[0;34mworkDir : [0;32m/home/sysgen/Desktop/ncct-projects/2201-Kostner-Assembly/work[0m
[0;34mprojectDir : [0;32m/home/sysgen/.nextflow/assets/nf-core/bacass[0m
[0;34muserName : [0;32msysgen[0m
[0;34mprofile : [0;32mdocker[0m
[0;34mconfigFiles : [0;32m/home/sysgen/.nextflow/assets/nf-core/bacass/nextflow.config[0m
[1mInput/output options[0m
[0;34minput : [0;32msamplesheet-bacass.csv[0m
[0;34moutdir : [0;32mresults[0m
[1mContamination Screening[0m
[0;34mkraken2db : [0;32m/home/sysgen/db/kraken/k2_pluspf_16gb_20210127.tar[0m
[1mAssembly parameters[0m
[0;34massembly_type : [0;32mhybrid[0m
[1mAnnotation[0m
[0;34mannotation_tool: [0;32mdfast[0m
[0;34mdfast_config : [0;32m/home/sysgen/.nextflow/assets/nf-core/bacass/assets/test_config_dfast.py[0m
!! Only displaying parameters that differ from the pipeline defaults !!
-[2m----------------------------------------------------[0m-
If you use nf-core/bacass for your analysis please cite:
* The pipeline
https://doi.org/10.5281/zenodo.2669428
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/bacass/blob/master/CITATIONS.md
-[2m----------------------------------------------------[0m-
Jan-19 08:48:50.358 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: FASTQC, MULTIQC, UNICYCLER, MINIMAP2_POLISH, PYCOQC, SAMTOOLS_SORT, SKEWER, PROKKA, MINIASM, KRAKEN2_KRAKEN2, QUAST, KRAKEN2_LONG, KRAKEN2_DB_PREPARATION, NANOPOLISH, KRAKEN2, GET_SOFTWARE_VERSIONS, RACON, MINIMAP2_CONSENSUS, MINIMAP2_ALIGN, CANU, MEDAKA, PORECHOP, NANOPLOT, SAMTOOLS_INDEX, DFAST
Jan-19 08:48:50.603 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_BACASS:BACASS:FASTQC
Jan-19 08:48:50.609 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-19 08:48:50.610 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-19 08:48:50.616 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jan-19 08:48:50.625 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=112; memory=1006.6 GB; capacity=112; pollInterval=100ms; dumpInterval=5m
Jan-19 08:48:50.731 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_BACASS:BACASS:SKEWER
Jan-19 08:48:50.732 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-19 08:48:50.733 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-19 08:48:50.748 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name NFCORE_BACASS:BACASS:NANOPLOT
Jan-19 08:48:50.750 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-19 08:48:50.751 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-19 08:48:50.765 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_BACASS:BACASS:PYCOQC
Jan-19 08:48:50.766 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-19 08:48:50.767 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-19 08:48:50.784 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_BACASS:BACASS:PORECHOP
Jan-19 08:48:50.786 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-19 08:48:50.786 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-19 08:48:50.815 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name NFCORE_BACASS:BACASS:UNICYCLER
Jan-19 08:48:50.816 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches label `process_long` for process with name NFCORE_BACASS:BACASS:UNICYCLER
Jan-19 08:48:50.816 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high_memory` matches label `process_high_memory` for process with name NFCORE_BACASS:BACASS:UNICYCLER
Jan-19 08:48:50.816 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_retry` matches label `error_retry` for process with name NFCORE_BACASS:BACASS:UNICYCLER
Jan-19 08:48:50.817 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-19 08:48:50.817 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-19 08:48:50.832 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name NFCORE_BACASS:BACASS:KRAKEN2_DB_PREPARATION
Jan-19 08:48:50.834 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-19 08:48:50.834 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-19 08:48:50.846 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name NFCORE_BACASS:BACASS:KRAKEN2
Jan-19 08:48:50.847 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches label `process_long` for process with name NFCORE_BACASS:BACASS:KRAKEN2
Jan-19 08:48:50.847 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high_memory` matches label `process_high_memory` for process with name NFCORE_BACASS:BACASS:KRAKEN2
Jan-19 08:48:50.849 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-19 08:48:50.849 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-19 08:48:50.870 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name NFCORE_BACASS:BACASS:KRAKEN2_LONG
Jan-19 08:48:50.870 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches label `process_long` for process with name NFCORE_BACASS:BACASS:KRAKEN2_LONG
Jan-19 08:48:50.870 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high_memory` matches label `process_high_memory` for process with name NFCORE_BACASS:BACASS:KRAKEN2_LONG
Jan-19 08:48:50.872 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-19 08:48:50.872 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-19 08:48:50.903 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_BACASS:BACASS:QUAST
Jan-19 08:48:50.905 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-19 08:48:50.906 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-19 08:48:50.925 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_BACASS:BACASS:DFAST
Jan-19 08:48:50.930 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-19 08:48:50.932 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-19 08:48:50.971 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-19 08:48:50.971 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-19 08:48:51.018 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_BACASS:BACASS:MULTIQC
Jan-19 08:48:51.019 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-19 08:48:51.020 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-19 08:48:51.031 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Jan-19 08:48:51.034 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Jan-19 08:48:51.034 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Jan-19 08:48:51.034 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Jan-19 08:48:51.035 [main] DEBUG nextflow.Session - Ignite dataflow network (21)
Jan-19 08:48:51.046 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_BACASS:BACASS:FASTQC
Jan-19 08:48:51.048 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_BACASS:BACASS:SKEWER
Jan-19 08:48:51.048 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_BACASS:BACASS:NANOPLOT
Jan-19 08:48:51.048 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_BACASS:BACASS:PYCOQC
Jan-19 08:48:51.049 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_BACASS:BACASS:PORECHOP
Jan-19 08:48:51.053 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_BACASS:BACASS:UNICYCLER
Jan-19 08:48:51.056 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_BACASS:BACASS:KRAKEN2_DB_PREPARATION
Jan-19 08:48:51.056 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_BACASS:BACASS:KRAKEN2
Jan-19 08:48:51.056 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_BACASS:BACASS:KRAKEN2_LONG
Jan-19 08:48:51.056 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_BACASS:BACASS:QUAST
Jan-19 08:48:51.056 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_BACASS:BACASS:DFAST
Jan-19 08:48:51.056 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_BACASS:BACASS:GET_SOFTWARE_VERSIONS
Jan-19 08:48:51.058 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_BACASS:BACASS:MULTIQC
Jan-19 08:48:51.059 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
Jan-19 08:48:51.060 [main] DEBUG nextflow.Session - Session await
Jan-19 08:48:51.317 [Actor Thread 6] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.002 s; external sort time: 0.025 s; total time: 0.027 s
Jan-19 08:48:51.327 [Actor Thread 6] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /tmp/a938744101fcc19ac3c3796a65915a9d.collect-file
Jan-19 08:48:51.342 [Actor Thread 6] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-5740245592786926266
Jan-19 08:48:51.372 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-19 08:48:51.382 [Task submitter] INFO nextflow.Session - [b6/5ee3ce] Submitted process > NFCORE_BACASS:BACASS:NANOPLOT (NS45)
Jan-19 08:48:51.415 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-19 08:48:51.416 [Task submitter] INFO nextflow.Session - [d3/784db9] Submitted process > NFCORE_BACASS:BACASS:PORECHOP (BioCat)
Jan-19 08:48:51.429 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-19 08:48:51.429 [Task submitter] INFO nextflow.Session - [b8/b8c971] Submitted process > NFCORE_BACASS:BACASS:KRAKEN2_DB_PREPARATION (k2_pluspf_16gb_20210127)
Jan-19 08:48:51.440 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-19 08:48:51.441 [Task submitter] INFO nextflow.Session - [eb/15cf32] Submitted process > NFCORE_BACASS:BACASS:PORECHOP (NS45)
Jan-19 08:48:51.451 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-19 08:48:51.452 [Task submitter] INFO nextflow.Session - [75/caa332] Submitted process > NFCORE_BACASS:BACASS:NANOPLOT (BioCat)
Jan-19 08:48:51.460 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-19 08:48:51.461 [Task submitter] INFO nextflow.Session - [07/523c9a] Submitted process > NFCORE_BACASS:BACASS:SKEWER (BioCat)
Jan-19 08:48:51.472 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-19 08:48:51.473 [Task submitter] INFO nextflow.Session - [0c/c653c6] Submitted process > NFCORE_BACASS:BACASS:FASTQC (BioCat)
Jan-19 08:48:51.484 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-19 08:48:51.485 [Task submitter] INFO nextflow.Session - [ae/09f3ab] Submitted process > NFCORE_BACASS:BACASS:FASTQC (NS45)
Jan-19 08:48:51.493 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-19 08:48:51.495 [Task submitter] INFO nextflow.Session - [f8/b60a7c] Submitted process > NFCORE_BACASS:BACASS:SKEWER (NS45)
Jan-19 08:49:51.577 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: NFCORE_BACASS:BACASS:NANOPLOT (NS45); status: COMPLETED; exit: 0; error: -; workDir: /home/sysgen/Desktop/ncct-projects/2201-Kostner-Assembly/work/b6/5ee3ce889e000a378cc359d94da18a]
Jan-19 08:49:51.612 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_BACASS:BACASS:NANOPLOT (NS45)'
Caused by:
Missing output file(s) `*.png` expected by process `NFCORE_BACASS:BACASS:NANOPLOT (NS45)`
Command executed:
NanoPlot \
\
-t 2 \
--fastq 2111-DK-l1-001.fastq
echo $(NanoPlot --version 2>&1) | sed 's/^.*NanoPlot //; s/ .*$//' > nanoplot.version.txt
Command exit status:
0
Command output:
(empty)
Work dir:
/home/sysgen/Desktop/ncct-projects/2201-Kostner-Assembly/work/b6/5ee3ce889e000a378cc359d94da18a
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Jan-19 08:49:51.688 [Task monitor] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit
Jan-19 08:49:51.706 [main] DEBUG nextflow.Session - Session await > all process finished
Jan-19 08:50:18.872 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: NFCORE_BACASS:BACASS:FASTQC (BioCat); status: COMPLETED; exit: 0; error: -; workDir: /home/sysgen/Desktop/ncct-projects/2201-Kostner-Assembly/work/0c/c653c615249feb3ed302be0dfbd0e2]
Jan-19 08:50:18.912 [Task monitor] DEBUG n.util.BlockingThreadExecutorFactory - Thread pool name=FileTransfer; maxThreads=336; maxQueueSize=1008; keepAlive=1m
Jan-19 08:50:19.002 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: NFCORE_BACASS:BACASS:FASTQC (NS45); status: COMPLETED; exit: 0; error: -; workDir: /home/sysgen/Desktop/ncct-projects/2201-Kostner-Assembly/work/ae/09f3abd23321176f059586a3327517]
Jan-19 08:50:26.449 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: NFCORE_BACASS:BACASS:NANOPLOT (BioCat); status: COMPLETED; exit: 0; error: -; workDir: /home/sysgen/Desktop/ncct-projects/2201-Kostner-Assembly/work/75/caa332172d1ed4f6c4b2e14bd64398]
Jan-19 08:50:53.047 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: NFCORE_BACASS:BACASS:KRAKEN2_DB_PREPARATION (k2_pluspf_16gb_20210127); status: COMPLETED; exit: 0; error: -; workDir: /home/sysgen/Desktop/ncct-projects/2201-Kostner-Assembly/work/b8/b8c97168af9a28aea8197b307f2254]
Jan-19 08:53:50.769 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 4 -- submitted tasks are shown below
~> TaskHandler[id: 6; name: NFCORE_BACASS:BACASS:PORECHOP (BioCat); status: RUNNING; exit: -; error: -; workDir: /home/sysgen/Desktop/ncct-projects/2201-Kostner-Assembly/work/d3/784db9aa45d4fc2b6b565c880481e7]
~> TaskHandler[id: 8; name: NFCORE_BACASS:BACASS:PORECHOP (NS45); status: RUNNING; exit: -; error: -; workDir: /home/sysgen/Desktop/ncct-projects/2201-Kostner-Assembly/work/eb/15cf324ea51f9e0625d7c324f72a9b]
~> TaskHandler[id: 4; name: NFCORE_BACASS:BACASS:SKEWER (BioCat); status: RUNNING; exit: -; error: -; workDir: /home/sysgen/Desktop/ncct-projects/2201-Kostner-Assembly/work/07/523c9affedb40a86567a21c0323832]
~> TaskHandler[id: 5; name: NFCORE_BACASS:BACASS:SKEWER (NS45); status: RUNNING; exit: -; error: -; workDir: /home/sysgen/Desktop/ncct-projects/2201-Kostner-Assembly/work/f8/b60a7c88c177ec3d2a795dd3872654]
Jan-19 08:55:14.931 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: NFCORE_BACASS:BACASS:PORECHOP (NS45); status: COMPLETED; exit: 0; error: -; workDir: /home/sysgen/Desktop/ncct-projects/2201-Kostner-Assembly/work/eb/15cf324ea51f9e0625d7c324f72a9b]
Jan-19 08:58:50.855 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 3 -- submitted tasks are shown below
~> TaskHandler[id: 6; name: NFCORE_BACASS:BACASS:PORECHOP (BioCat); status: RUNNING; exit: -; error: -; workDir: /home/sysgen/Desktop/ncct-projects/2201-Kostner-Assembly/work/d3/784db9aa45d4fc2b6b565c880481e7]
~> TaskHandler[id: 4; name: NFCORE_BACASS:BACASS:SKEWER (BioCat); status: RUNNING; exit: -; error: -; workDir: /home/sysgen/Desktop/ncct-projects/2201-Kostner-Assembly/work/07/523c9affedb40a86567a21c0323832]
~> TaskHandler[id: 5; name: NFCORE_BACASS:BACASS:SKEWER (NS45); status: RUNNING; exit: -; error: -; workDir: /home/sysgen/Desktop/ncct-projects/2201-Kostner-Assembly/work/f8/b60a7c88c177ec3d2a795dd3872654]
Jan-19 08:59:42.031 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: NFCORE_BACASS:BACASS:PORECHOP (BioCat); status: COMPLETED; exit: 0; error: -; workDir: /home/sysgen/Desktop/ncct-projects/2201-Kostner-Assembly/work/d3/784db9aa45d4fc2b6b565c880481e7]
Jan-19 09:00:18.671 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: NFCORE_BACASS:BACASS:SKEWER (BioCat); status: COMPLETED; exit: 0; error: -; workDir: /home/sysgen/Desktop/ncct-projects/2201-Kostner-Assembly/work/07/523c9affedb40a86567a21c0323832]
Jan-19 09:00:38.752 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: NFCORE_BACASS:BACASS:SKEWER (NS45); status: COMPLETED; exit: 0; error: -; workDir: /home/sysgen/Desktop/ncct-projects/2201-Kostner-Assembly/work/f8/b60a7c88c177ec3d2a795dd3872654]
Jan-19 09:00:38.768 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jan-19 09:00:38.774 [main] INFO nextflow.Nextflow - -[0;35m[nf-core/bacass][0;31m Pipeline completed with errors[0m-
Jan-19 09:00:39.079 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=7; failedCount=2; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=5h 43m 47s; failedDuration=4m 38s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=9; peakCpus=54; peakMemory=51 GB; ]
Jan-19 09:00:39.080 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file
Jan-19 09:00:39.083 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report
Jan-19 09:00:39.156 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
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Jan-19 09:00:40.285 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline
Jan-19 09:00:40.796 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
Jan-19 09:00:40.826 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye