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.nextflow.log.4
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Oct-05 16:21:55.029 [main] DEBUG nextflow.cli.Launcher - $> nextflow run pipeline.nf -with-singularity 'snpEff:5.0.sif'
Oct-05 16:21:55.133 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 22.10.7
Oct-05 16:21:55.176 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/guest/.nextflow/plugins; core-plugins: [email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected]
Oct-05 16:21:55.189 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Oct-05 16:21:55.190 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Oct-05 16:21:55.193 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Oct-05 16:21:55.208 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Oct-05 16:21:55.265 [main] DEBUG nextflow.config.ConfigBuilder - Enabling execution in Singularity container as requested by command-line option `-with-singularity null`
Oct-05 16:21:55.285 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
Oct-05 16:21:55.306 [main] INFO nextflow.cli.CmdRun - Launching `pipeline.nf` [irreverent_thompson] DSL2 - revision: 8451c4e07a
Oct-05 16:21:55.307 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Oct-05 16:21:55.307 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Oct-05 16:21:55.319 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /home/guest/.nextflow/secrets/store.json
Oct-05 16:21:55.322 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@3d7fa3ae] - activable => nextflow.secret.LocalSecretsProvider@3d7fa3ae
Oct-05 16:21:55.422 [main] DEBUG nextflow.Session - Session UUID: 77452032-bc23-4a39-b903-a873778565f0
Oct-05 16:21:55.422 [main] DEBUG nextflow.Session - Run name: irreverent_thompson
Oct-05 16:21:55.422 [main] DEBUG nextflow.Session - Executor pool size: 6
Oct-05 16:21:55.436 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=18; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Oct-05 16:21:55.469 [main] DEBUG nextflow.cli.CmdRun -
Version: 22.10.7 build 5853
Created: 18-02-2023 20:32 UTC (21:32 CEST)
System: Linux 6.2.11-100.fc36.x86_64
Runtime: Groovy 3.0.13 on OpenJDK 64-Bit Server VM 17.0.6+10
Encoding: UTF-8 (UTF-8)
Process: 325978@fedora [10.0.2.15]
CPUs: 6 - Mem: 7.7 GB (1 GB) - Swap: 7.7 GB (5.3 GB)
Oct-05 16:21:55.498 [main] DEBUG nextflow.Session - Work-dir: /home/guest/snpEff/PIPE/work [btrfs]
Oct-05 16:21:55.499 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/guest/snpEff/PIPE/bin
Oct-05 16:21:55.509 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Oct-05 16:21:55.546 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Oct-05 16:21:55.572 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Oct-05 16:21:55.585 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 7; maxThreads: 1000
Oct-05 16:21:55.662 [main] DEBUG nextflow.Session - Session start
Oct-05 16:21:56.467 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Oct-05 16:21:56.644 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-05 16:21:56.644 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-05 16:21:56.653 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Oct-05 16:21:56.658 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=6; memory=7.7 GB; capacity=6; pollInterval=100ms; dumpInterval=5m
Oct-05 16:21:56.806 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: snpEff
Oct-05 16:21:56.806 [main] DEBUG nextflow.Session - Igniting dataflow network (1)
Oct-05 16:21:56.806 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snpEff
Oct-05 16:21:56.807 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Oct-05 16:21:56.807 [main] DEBUG nextflow.Session - Session await
Oct-05 16:21:57.007 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-05 16:21:57.010 [Task submitter] INFO nextflow.Session - [46/a449c2] Submitted process > snpEff
Oct-05 16:21:59.336 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: snpEff; status: COMPLETED; exit: 255; error: -; workDir: /home/guest/snpEff/PIPE/work/46/a449c20cbd4749de7f4773cb0fb24a]
Oct-05 16:21:59.353 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'snpEff'
Caused by:
Process `snpEff` terminated with an error exit status (255)
Command executed:
java -jar /usr/local/share/snpeff-5.0-0/snpEff.jar -i vcf -o vcf -fastaProt out.fa 00_INPUT/in.vcf > out.vcf
Command exit status:
255
Command output:
(empty)
Command error:
WARNING: Skipping mount /var/apptainer/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
java.lang.RuntimeException: Property: '00_INPUT/in.vcf.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:104)
at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:681)
at org.snpeff.snpEffect.Config.readConfig(Config.java:649)
at org.snpeff.snpEffect.Config.init(Config.java:480)
at org.snpeff.snpEffect.Config.<init>(Config.java:117)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:456)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:938)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:922)
at org.snpeff.SnpEff.run(SnpEff.java:1194)
at org.snpeff.SnpEff.main(SnpEff.java:167)
Work dir:
/home/guest/snpEff/PIPE/work/46/a449c20cbd4749de7f4773cb0fb24a
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Oct-05 16:21:59.361 [main] DEBUG nextflow.Session - Session await > all processes finished
Oct-05 16:21:59.365 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process `snpEff` terminated with an error exit status (255)
Oct-05 16:21:59.381 [main] DEBUG nextflow.Session - Session await > all barriers passed
Oct-05 16:21:59.396 [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=2.3s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=0; ]
Oct-05 16:21:59.576 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Oct-05 16:21:59.591 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye