example5 doesn't work

[KateSakharova]

Hi,

I've cloned repo and launched example5 run.sh. It returned me error

ERROR ~ Error executing process > 'foo'

Caused by:
  Process `foo` terminated with an error exit status (127)

Command executed:

  say-hello.sh

Command exit status:
  127

Command output:
  (empty)

Command error:
  Unable to find image 'wave.seqera.io/wt/613efa5ba765/nextflow/bash:latest' locally
  latest: Pulling from wt/613efa5ba765/nextflow/bash
  Digest: sha256:3cfc6c8805e65b6196f591782498bd978e9d7c43090b88161c9e343f1a67b85c
  Status: Downloaded newer image for wave.seqera.io/wt/613efa5ba765/nextflow/bash:latest
  .command.sh: line 2: say-hello.sh: command not found

Nextflow version: Nextflow 24.02.0-edge

Best,
Ekaterina

[pditommaso]

Weird. Just tried at it looks ok. Can you please include the .nextflow.log file?

[KateSakharova]

Apr-15 14:57:15.371 [main] DEBUG nextflow.cli.Launcher - $> nextflow run demo.nf -with-wave
Apr-15 14:57:15.571 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W  ~  version 24.03.0-edge
Apr-15 14:57:15.624 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/Users/kates/.nextflow/plugins; core-plugins: [email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected]
Apr-15 14:57:15.653 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Apr-15 14:57:15.654 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Apr-15 14:57:15.659 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.10.0 in 'deployment' mode
Apr-15 14:57:15.697 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Apr-15 14:57:15.789 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /Users/kates/PycharmProjects/test-scripts/Nextflow/wave-showcase/example5/nextflow.config
Apr-15 14:57:15.796 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/kates/PycharmProjects/test-scripts/Nextflow/wave-showcase/example5/nextflow.config
Apr-15 14:57:15.887 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /Users/kates/.nextflow/secrets/store.json
Apr-15 14:57:15.895 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@3a60c416] - activable => nextflow.secret.LocalSecretsProvider@3a60c416
Apr-15 14:57:15.918 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Apr-15 14:57:17.002 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
Apr-15 14:57:17.019 [main] DEBUG nextflow.cli.CmdRun - Launching `demo.nf` [festering_legentil] DSL2 - revision: d33d41be15
Apr-15 14:57:17.023 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Apr-15 14:57:17.025 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[[email protected]]
Apr-15 14:57:17.026 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-wave version: 1.4.0
Apr-15 14:57:17.042 [main] INFO  org.pf4j.AbstractPluginManager - Plugin '[email protected]' resolved
Apr-15 14:57:17.042 [main] INFO  org.pf4j.AbstractPluginManager - Start plugin '[email protected]'
Apr-15 14:57:17.098 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started [email protected]
Apr-15 14:57:17.203 [main] DEBUG nextflow.Session - Session UUID: 2461723f-a2d9-4494-8250-273e44b43c67
Apr-15 14:57:17.204 [main] DEBUG nextflow.Session - Run name: festering_legentil
Apr-15 14:57:17.205 [main] DEBUG nextflow.Session - Executor pool size: 8
Apr-15 14:57:17.215 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Apr-15 14:57:17.220 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Apr-15 14:57:17.414 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 24.03.0-edge build 5908
  Created: 15-04-2024 09:12 UTC (10:12 BST)
  System: Mac OS X 14.4.1
  Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 17.0.3+7-LTS
  Encoding: UTF-8 (UTF-8)
  Process: 3824@HL02Q4M9HW [192.168.0.19]
  CPUs: 8 - Mem: 24 GB (17 MB) - Swap: 7 GB (1.2 GB)
Apr-15 14:57:17.463 [main] DEBUG nextflow.Session - Work-dir: /Users/kates/PycharmProjects/test-scripts/Nextflow/wave-showcase/example5/work [Mac OS X]
Apr-15 14:57:17.464 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /Users/kates/PycharmProjects/test-scripts/Nextflow/wave-showcase/example5/bin
Apr-15 14:57:17.479 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Apr-15 14:57:17.498 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Apr-15 14:57:17.503 [main] DEBUG nextflow.Session - Observer factory: WaveFactory
Apr-15 14:57:17.525 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Apr-15 14:57:17.538 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000
Apr-15 14:57:17.595 [main] DEBUG nextflow.Session - Session start
Apr-15 14:57:17.896 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Apr-15 14:57:18.175 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Apr-15 14:57:18.176 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Apr-15 14:57:18.185 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Apr-15 14:57:18.191 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=8; memory=24 GB; capacity=8; pollInterval=100ms; dumpInterval=5m
Apr-15 14:57:18.194 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Apr-15 14:57:18.316 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: foo
Apr-15 14:57:18.317 [main] DEBUG nextflow.Session - Igniting dataflow network (1)
Apr-15 14:57:18.317 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > foo
Apr-15 14:57:18.318 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
  Script_ee94fc1788ba84ec: /Users/kates/PycharmProjects/test-scripts/Nextflow/wave-showcase/example5/demo.nf
  Script_c36104345fee2511: /Users/kates/PycharmProjects/test-scripts/Nextflow/wave-showcase/example5/./modules/foo/main.nf
Apr-15 14:57:18.318 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination 
Apr-15 14:57:18.318 [main] DEBUG nextflow.Session - Session await
Apr-15 14:57:18.445 [Actor Thread 3] DEBUG i.s.wave.plugin.config.WaveConfig - Wave strategy not specified - using default: [container, dockerfile, conda, spack]
Apr-15 14:57:18.455 [Actor Thread 3] DEBUG io.seqera.wave.plugin.WaveClient - Wave config: WaveConfig(enabled:true, endpoint:https://wave.seqera.io, containerConfigUrl:[], tokensCacheMaxDuration:30m, condaOpts:CondaOpts(mambaImage=mambaorg/micromamba:1.5.8-lunar; basePackages=conda-forge::procps-ng, commands=null), spackOpts:SpackOpts(basePackages=null, commands=null), strategy:[container, dockerfile, conda, spack], bundleProjectResources:null, buildRepository:null, cacheRepository:null, retryOpts:RetryOpts(delay:450ms, maxDelay:1m 30s, maxAttempts:10, jitter:0.25), httpClientOpts:HttpOpts(), freezeMode:null, preserveFileTimestamp:null)
Apr-15 14:57:18.853 [Actor Thread 3] DEBUG io.seqera.wave.plugin.WaveClient - Wave request: https://wave.seqera.io/v1alpha2/container; attempt=1 - request: SubmitContainerTokenRequest(towerAccessToken:null, towerRefreshToken:null, towerWorkspaceId:null, towerEndpoint:https://api.cloud.seqera.io, containerImage:quay.io/nextflow/bash, containerFile:null, containerConfig:ContainerConfig(entrypoint:null, cmd:null, env:null, workingDir:null, layers:[ContainerLayer[location=data:H4sIAAAAAAAA/+2S0QrC...; tarDigest=sha256:352a564556269049fefd7719355f1e1ee653baeeeedc720c86af0576dc21879c; gzipDigest=sha256:ac06d5969b2d758dc273047773dcbc037958537ea724d308bf8609276806350e; gzipSize=183]]), condaFile:null, spackFile:null, containerPlatform:linux/amd64, buildRepository:null, cacheRepository:null, timestamp:2024-04-15T14:57:18.815477+01:00, fingerprint:ce76acd4cff99a9868c5c1ca019f2edd, freeze:false, format:null, dryRun:false, workflowId:null, containerIncludes:null, packages:null)
Apr-15 14:57:19.576 [Actor Thread 3] DEBUG io.seqera.wave.plugin.WaveClient - Wave response: statusCode=200; body={"containerToken":"744a286e7aab","targetImage":"wave.seqera.io/wt/744a286e7aab/nextflow/bash:latest","expiration":"2024-04-17T01:57:19.552568341Z","containerImage":"quay.io/nextflow/bash:latest","cached":true,"freeze":false}
Apr-15 14:57:19.895 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Apr-15 14:57:19.898 [Task submitter] INFO  nextflow.Session - [f6/ce2bf6] Submitted process > foo
Apr-15 14:57:22.480 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: foo; status: COMPLETED; exit: 127; error: -; workDir: /Users/kates/PycharmProjects/test-scripts/Nextflow/wave-showcase/example5/work/f6/ce2bf61ae7c79e6ad1ae85539277e4]
Apr-15 14:57:22.493 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=foo; work-dir=/Users/kates/PycharmProjects/test-scripts/Nextflow/wave-showcase/example5/work/f6/ce2bf61ae7c79e6ad1ae85539277e4
  error [nextflow.exception.ProcessFailedException]: Process `foo` terminated with an error exit status (127)
Apr-15 14:57:22.523 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'foo'

Caused by:
  Process `foo` terminated with an error exit status (127)

Command executed:

  say-hello.sh

Command exit status:
  127

Command output:
  (empty)

Command error:
  Unable to find image 'wave.seqera.io/wt/744a286e7aab/nextflow/bash:latest' locally
  latest: Pulling from wt/744a286e7aab/nextflow/bash
  Digest: sha256:3cfc6c8805e65b6196f591782498bd978e9d7c43090b88161c9e343f1a67b85c
  Status: Downloaded newer image for wave.seqera.io/wt/744a286e7aab/nextflow/bash:latest
  .command.sh: line 2: say-hello.sh: command not found

Work dir:
  /Users/kates/PycharmProjects/test-scripts/Nextflow/wave-showcase/example5/work/f6/ce2bf61ae7c79e6ad1ae85539277e4

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
Apr-15 14:57:22.536 [main] DEBUG nextflow.Session - Session await > all processes finished
Apr-15 14:57:22.552 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process `foo` terminated with an error exit status (127)
Apr-15 14:57:22.609 [main] DEBUG nextflow.Session - Session await > all barriers passed
Apr-15 14:57:22.610 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Apr-15 14:57:22.623 [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=2.5s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=0; ]
Apr-15 14:57:22.784 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Apr-15 14:57:22.786 [main] INFO  org.pf4j.AbstractPluginManager - Stop plugin '[email protected]'
Apr-15 14:57:22.786 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-wave
Apr-15 14:57:22.813 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

[pditommaso]

Any chance you can also tar and upload the content of the /Users/kates/PycharmProjects/test-scripts/Nextflow/wave-showcase/example5/work/f6/ce2bf61ae7c79e6ad1ae85539277e4 directory ?

[KateSakharova]

logs.tar.gz

[pditommaso]

Really not understanding, trying to the script is accessible in the container

» docker run wave.seqera.io/wt/744a286e7aab/nextflow/bash:latest /bin/bash -c 'say-hello.sh'
Hello world!

@bentsherman any clue what could be wrong?

[bentsherman]

Not sure 🤷 is the moduleBinaries feature flag not required when using Wave?

[pditommaso]

Nope it's implicit when using Wave