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.nextflow.log.8
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Oct-22 23:04:52.055 [main] DEBUG nextflow.cli.Launcher - $> nextflow run code/spletter_nextflow.nf
Oct-22 23:04:52.100 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.10.1
Oct-22 23:04:52.110 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/drinnan/.nextflow/plugins; core-plugins: [email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected]
Oct-22 23:04:52.116 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Oct-22 23:04:52.116 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Oct-22 23:04:52.118 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Oct-22 23:04:52.124 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Oct-22 23:04:52.166 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Oct-22 23:04:52.176 [main] INFO nextflow.cli.CmdRun - Launching `code/spletter_nextflow.nf` [high_brattain] DSL2 - revision: c100e58921
Oct-22 23:04:52.176 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Oct-22 23:04:52.176 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Oct-22 23:04:52.182 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/drinnan/.nextflow/secrets/store.json
Oct-22 23:04:52.186 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@18a645fd] - activable => nextflow.secret.LocalSecretsProvider@18a645fd
Oct-22 23:04:52.224 [main] DEBUG nextflow.Session - Session UUID: 6e12781d-1c45-4bf5-b528-7f8a51620a57
Oct-22 23:04:52.224 [main] DEBUG nextflow.Session - Run name: high_brattain
Oct-22 23:04:52.225 [main] DEBUG nextflow.Session - Executor pool size: 20
Oct-22 23:04:52.230 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Oct-22 23:04:52.246 [main] DEBUG nextflow.cli.CmdRun -
Version: 23.10.1 build 5891
Created: 12-01-2024 22:01 UTC (16:01 CDT)
System: Linux 6.2.6-76060206-generic
Runtime: Groovy 3.0.19 on OpenJDK 64-Bit Server VM 21.0.2+13-Ubuntu-122.04.1
Encoding: UTF-8 (UTF-8)
Process: 25999@pop-os [127.0.1.1]
CPUs: 20 - Mem: 31 GB (1.1 GB) - Swap: 20 GB (20 GB) - Virtual threads ON
Oct-22 23:04:52.259 [main] DEBUG nextflow.Session - Work-dir: /home/drinnan/projects/spletter_lrRNA/work [ext2/ext3]
Oct-22 23:04:52.259 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/drinnan/projects/spletter_lrRNA/code/bin
Oct-22 23:04:52.265 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Oct-22 23:04:52.271 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Oct-22 23:04:52.285 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Oct-22 23:04:52.290 [main] DEBUG nextflow.util.CustomPoolFactory - Creating virtual thread pool
Oct-22 23:04:52.360 [main] DEBUG nextflow.Session - Session start
Oct-22 23:04:52.803 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Oct-22 23:04:52.882 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-22 23:04:52.882 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-22 23:04:52.886 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Oct-22 23:04:52.890 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=20; memory=31 GB; capacity=20; pollInterval=100ms; dumpInterval=5m
Oct-22 23:04:52.891 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Oct-22 23:04:52.944 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: bam_index, kraken2, kraken_uniq, fastqc, qualimap, unmapped_read_extraction
Oct-22 23:04:52.944 [main] DEBUG nextflow.Session - Igniting dataflow network (2)
Oct-22 23:04:52.948 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > fastqc
Oct-22 23:04:52.948 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_39f8458576dc3c7c: /home/drinnan/projects/spletter_lrRNA/code/spletter_nextflow.nf
Oct-22 23:04:52.948 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Oct-22 23:04:52.949 [main] DEBUG nextflow.Session - Session await
Oct-22 23:04:52.949 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /home/drinnan/projects/test_data/; pattern: *fastq; options: [:]
Oct-22 23:04:52.951 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - No such file or directory: /home/drinnan/projects/test_data/ -- Skipping visit
Oct-22 23:04:52.957 [main] DEBUG nextflow.Session - Session await > all processes finished
Oct-22 23:04:52.995 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Oct-22 23:04:52.996 [main] DEBUG nextflow.Session - Session await > all barriers passed
Oct-22 23:04:52.998 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ]
Oct-22 23:04:53.190 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Oct-22 23:04:53.203 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Oct-22 23:04:53.203 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye