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.nextflow.log.3
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Oct-22 23:37:43.371 [main] DEBUG nextflow.cli.Launcher - $> nextflow run code/spletter_nextflow.nf -with-conda
Oct-22 23:37:43.444 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.10.1
Oct-22 23:37:43.462 [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 23:37:43.475 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Oct-22 23:37:43.476 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Oct-22 23:37:43.479 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Oct-22 23:37:43.489 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Oct-22 23:37:43.554 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Oct-22 23:37:43.572 [main] INFO nextflow.cli.CmdRun - Launching `code/spletter_nextflow.nf` [trusting_bernard] DSL2 - revision: 52896ec368
Oct-22 23:37:43.573 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Oct-22 23:37:43.573 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Oct-22 23:37:43.581 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/drinnan/.nextflow/secrets/store.json
Oct-22 23:37:43.588 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@18a645fd] - activable => nextflow.secret.LocalSecretsProvider@18a645fd
Oct-22 23:37:43.653 [main] DEBUG nextflow.Session - Session UUID: fb15269c-363a-43b1-bae0-5dbf4ed2b4d9
Oct-22 23:37:43.653 [main] DEBUG nextflow.Session - Run name: trusting_bernard
Oct-22 23:37:43.655 [main] DEBUG nextflow.Session - Executor pool size: 20
Oct-22 23:37:43.663 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Oct-22 23:37:43.691 [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: 30883@pop-os [127.0.1.1]
CPUs: 20 - Mem: 31 GB (2.8 GB) - Swap: 20 GB (20 GB) - Virtual threads ON
Oct-22 23:37:43.718 [main] DEBUG nextflow.Session - Work-dir: /home/drinnan/projects/spletter_lrRNA/work [ext2/ext3]
Oct-22 23:37:43.719 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/drinnan/projects/spletter_lrRNA/code/bin
Oct-22 23:37:43.729 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Oct-22 23:37:43.741 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Oct-22 23:37:43.765 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Oct-22 23:37:43.775 [main] DEBUG nextflow.util.CustomPoolFactory - Creating virtual thread pool
Oct-22 23:37:43.859 [main] DEBUG nextflow.Session - Session start
Oct-22 23:37:44.704 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Oct-22 23:37:44.849 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-22 23:37:44.849 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-22 23:37:44.855 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Oct-22 23:37:44.862 [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 23:37:44.865 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Oct-22 23:37:44.933 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: bam_index, kraken2, kraken_uniq, qualimap, unmapped_read_extraction, NanoPlot
Oct-22 23:37:44.933 [main] DEBUG nextflow.Session - Igniting dataflow network (2)
Oct-22 23:37:44.937 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NanoPlot
Oct-22 23:37:44.938 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_48fc5bffd4d11eba: /home/drinnan/projects/spletter_lrRNA/code/spletter_nextflow.nf
Oct-22 23:37:44.938 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Oct-22 23:37:44.938 [main] DEBUG nextflow.Session - Session await
Oct-22 23:37:45.023 [Actor Thread 8] DEBUG nextflow.conda.CondaCache - conda found local env for environment=/home/drinnan/miniconda3/envs/spletter; path=/home/drinnan/miniconda3/envs/spletter
Oct-22 23:37:45.028 [Actor Thread 6] DEBUG nextflow.util.CacheHelper - Unable to get file attributes file: /home/drinnan/projects/spletter/test_data/downsampled_10000.fastq -- Cause: java.nio.file.NoSuchFileException: /home/drinnan/projects/spletter/test_data/downsampled_10000.fastq
Oct-22 23:37:45.122 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-22 23:37:45.124 [Task submitter] INFO nextflow.Session - [a4/4a4ddc] Submitted process > NanoPlot (downsampled_10000)
Oct-22 23:37:46.051 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: NanoPlot (downsampled_10000); status: COMPLETED; exit: 1; error: -; workDir: /home/drinnan/projects/spletter_lrRNA/work/a4/4a4ddcb4e969b5c53a94de62f6577d]
Oct-22 23:37:46.054 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=NanoPlot (downsampled_10000); work-dir=/home/drinnan/projects/spletter_lrRNA/work/a4/4a4ddcb4e969b5c53a94de62f6577d
error [nextflow.exception.ProcessFailedException]: Process `NanoPlot (downsampled_10000)` terminated with an error exit status (1)
Oct-22 23:37:46.064 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NanoPlot (downsampled_10000)'
Caused by:
Process `NanoPlot (downsampled_10000)` terminated with an error exit status (1)
Command executed:
NanoPlot --fastq downsampled_10000.fastq
Command exit status:
1
Command output:
(empty)
Command error:
File provided doesn't exist or the path is incorrect: downsampled_10000.fastq
Work dir:
/home/drinnan/projects/spletter_lrRNA/work/a4/4a4ddcb4e969b5c53a94de62f6577d
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Oct-22 23:37:46.069 [main] DEBUG nextflow.Session - Session await > all processes finished
Oct-22 23:37:46.069 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process `NanoPlot (downsampled_10000)` terminated with an error exit status (1)
Oct-22 23:37:46.081 [main] DEBUG nextflow.Session - Session await > all barriers passed
Oct-22 23:37:46.082 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Oct-22 23:37:46.086 [main] DEBUG n.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=879ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=0; ]
Oct-22 23:37:46.286 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Oct-22 23:37:46.299 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye