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Error in test run #61

Closed dnaase closed 5 months ago

dnaase commented 5 months ago

Operating System

CentOS 7

Other Linux

No response

Workflow Version

v24.04.2

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-pore-c \ --bam wf-pore-c-demo/porec_test.concatemers.bam --chunk_size 100 \ --ref wf-pore-c-demo/porec_test.fasta \ --cutter NlaIII \ --vcf wf-pore-c-demo/porec_test.phased_variants.vcf.gz \ --paired_end_minimum_distance 100 --paired_end_maximum_distance 200 --hi_c --mcool --paired_end

Workflow Execution - CLI Execution Profile

standard (default)

What happened?

It report bugs with the following msg:

N E X T F L O W ~ version 24.04.2

Launching https://github.com/epi2me-labs/wf-pore-c [hopeful_pike] DSL2 - revision: a4ffadaaa9 [master]

ERROR ~ Script compilation error

1 error

-- Check '.nextflow.log' file for details

Relevant log output

N E X T F L O W   ~  version 24.04.2

Launching `https://github.com/epi2me-labs/wf-pore-c` [hopeful_pike] DSL2 - revision: a4ffadaaa9 [master]

Jun-04 10:56:24.450 [main] DEBUG nextflow.cli.Launcher - $> nextflow run epi2me-labs/wf-pore-c --bam wf-pore-c-demo/porec_test.concatemers.bam --chunk_size 100 --ref wf-pore-c-demo/porec_test.fasta --cutter NlaIII --vcf wf-pore-c-demo/porec_test.phased_variants.vcf.gz --paired_end_minimum_distance 100 --paired_end_maximum_distance 200 --hi_c --mcool --paired_end
Jun-04 10:56:24.561 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W  ~  version 24.04.2
Jun-04 10:56:24.583 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/xfj2191/.nextflow/plugins; core-plugins: nf-amazon@2.5.2,nf-azure@1.6.0,nf-cloudcache@0.4.1,nf-codecommit@0.2.0,nf-console@1.1.3,nf-ga4gh@1.3.0,nf-google@1.13.2,nf-tower@1.9.1,nf-wave@1.4.2
Jun-04 10:56:24.594 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jun-04 10:56:24.595 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jun-04 10:56:24.599 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.10.0 in 'deployment' mode
Jun-04 10:56:24.611 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Jun-04 10:56:24.624 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/xfj2191/.nextflow/scm
Jun-04 10:56:25.494 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/xfj2191/.nextflow/assets/epi2me-labs/wf-pore-c/.git/config; branch: master; remote: origin; url: https://github.com/epi2me-labs/wf-pore-c.git
Jun-04 10:56:25.525 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Jun-04 10:56:25.535 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/xfj2191/.nextflow/assets/epi2me-labs/wf-pore-c/.git/config; branch: master; remote: origin; url: https://github.com/epi2me-labs/wf-pore-c.git
Jun-04 10:56:26.250 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/xfj2191/.nextflow/assets/epi2me-labs/wf-pore-c/nextflow.config
Jun-04 10:56:26.253 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/xfj2191/.nextflow/assets/epi2me-labs/wf-pore-c/nextflow.config
Jun-04 10:56:26.263 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/xfj2191/.nextflow/secrets/store.json
Jun-04 10:56:26.265 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@5ed5b321] - activable => nextflow.secret.LocalSecretsProvider@5ed5b321
Jun-04 10:56:26.278 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Jun-04 10:56:26.522 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Jun-04 10:56:26.523 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/epi2me-labs/wf-pore-c` [voluminous_perlman] DSL2 - revision: a4ffadaaa9 [master]
Jun-04 10:56:26.524 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jun-04 10:56:26.524 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jun-04 10:56:26.580 [main] DEBUG nextflow.Session - Session UUID: 08a9842c-b27c-4619-9f10-a685d1451028
Jun-04 10:56:26.581 [main] DEBUG nextflow.Session - Run name: voluminous_perlman
Jun-04 10:56:26.581 [main] DEBUG nextflow.Session - Executor pool size: 5
Jun-04 10:56:26.590 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jun-04 10:56:26.594 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=15; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jun-04 10:56:26.614 [main] DEBUG nextflow.cli.CmdRun -
  Version: 24.04.2 build 5914
  Created: 29-05-2024 06:19 UTC (01:19 CDT)
  System: Linux 3.10.0-1160.95.1.el7.x86_64
  Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 17.0.2+8
  Encoding: UTF-8 (ANSI_X3.4-1968)
  Process: 66723@qnode0137 [172.20.138.37]
  CPUs: 5 - Mem: 20 GB (19.7 GB) - Swap: 0 (0)
Jun-04 10:56:26.635 [main] DEBUG nextflow.Session - Work-dir: /projects/b1198/epifluidlab/yaping/projects/porec_gm_20240602/test/work [gpfs]
Jun-04 10:56:26.720 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jun-04 10:56:26.732 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jun-04 10:56:26.795 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jun-04 10:56:26.804 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 6; maxThreads: 1000
Jun-04 10:56:26.929 [main] DEBUG nextflow.Session - Session start
Jun-04 10:56:26.935 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /projects/b1198/epifluidlab/yaping/projects/porec_gm_20240602/test/output/execution/trace.txt
Jun-04 10:56:26.966 [main] DEBUG nextflow.Session - Using default localLib path: /home/xfj2191/.nextflow/assets/epi2me-labs/wf-pore-c/lib
Jun-04 10:56:26.975 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/xfj2191/.nextflow/assets/epi2me-labs/wf-pore-c/lib
Jun-04 10:56:26.976 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/xfj2191/.nextflow/assets/epi2me-labs/wf-pore-c/lib/nfcore_external_java_deps.jar
Jun-04 10:56:27.869 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Jun-04 10:56:27.875 [main] ERROR nextflow.cli.Launcher - Script compilation error
- file : /home/xfj2191/.nextflow/assets/epi2me-labs/wf-pore-c/main.nf
- cause: Invalid output definition @ line 386, column 5.
       output(POREC.out.stats)
       ^

1 error

nextflow.exception.ScriptCompilationException: Script compilation error
- file : /home/xfj2191/.nextflow/assets/epi2me-labs/wf-pore-c/main.nf
- cause: Invalid output definition @ line 386, column 5.
       output(POREC.out.stats)
       ^

1 error

        at nextflow.script.ScriptParser.parse0(ScriptParser.groovy:196)
        at nextflow.script.ScriptParser.parse(ScriptParser.groovy:206)
        at nextflow.script.ScriptRunner.parseScript(ScriptRunner.groovy:229)
        at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:136)
        at nextflow.cli.CmdRun.run(CmdRun.groovy:372)
        at nextflow.cli.Launcher.run(Launcher.groovy:503)
        at nextflow.cli.Launcher.main(Launcher.groovy:657)
Caused by: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
Script_6183ff06cb5d1fd0: 386: Invalid output definition @ line 386, column 5.
       output(POREC.out.stats)
       ^

1 error

        at org.codehaus.groovy.control.ErrorCollector.failIfErrors(ErrorCollector.java:292)
        at org.codehaus.groovy.control.CompilationUnit$IPrimaryClassNodeOperation.doPhaseOperation(CompilationUnit.java:980)
        at org.codehaus.groovy.control.CompilationUnit.processPhaseOperations(CompilationUnit.java:692)
        at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:666)
        at groovy.lang.GroovyClassLoader.doParseClass(GroovyClassLoader.java:373)
        at groovy.lang.GroovyClassLoader.lambda$parseClass$2(GroovyClassLoader.java:316)
        at org.codehaus.groovy.runtime.memoize.StampedCommonCache.compute(StampedCommonCache.java:163)
        at org.codehaus.groovy.runtime.memoize.StampedCommonCache.getAndPut(StampedCommonCache.java:154)
        at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:314)
        at groovy.lang.GroovyShell.parseClass(GroovyShell.java:572)
        at groovy.lang.GroovyShell.parse(GroovyShell.java:585)
        at groovy.lang.GroovyShell.parse(GroovyShell.java:639)
        at groovy.lang.GroovyShell.parse(GroovyShell.java:643)
        at nextflow.script.ScriptParser.parse0(ScriptParser.groovy:175)
        ... 6 common frames omitted

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

no

Other demo data information

wf-pore-c-demo.tar.gz
sarahjeeeze commented 5 months ago

Hi, thanks for reporting this, this workflow is untested with the latest version of nextflow we have a fix coming soon. In the meantime you could run it with 23.04.2

dnaase commented 5 months ago

It works now! Thanks a lot!