API tools faq
paste
Advertisement
Guest User

Untitled

a guest
Dec 8th, 2017
112
0
Never
Add comment
Not a member of Pastebin yet? Sign Up, it unlocks many cool features!
Groovy 8.08 KB | None | 0 0
raw download clone embed print report
  1. Dec-08 12:07:31.248 [main] DEBUG nextflow.cli.Launcher - $> /usr/local/bin/nextflow run ../main.nf -resume -name Test RNA Run: 1512731087 -profile docker --max_memory 7.GB --max_cpus 2 --max_time 48h --gtf ./test_data/ngi-rna_test_set/genes.gtf --bed12 ./test_data/ngi-rna_test_set/genes.bed --hisat2_index ./test_data/ngi-rna_test_set/r64/ --aligner hisat2 --singleEnd --reads ./test_data/ngi-rna_test_set/*.fastq.gz
  2. Dec-08 12:07:31.385 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 0.25.7
  3. Dec-08 12:07:31.413 [main] INFO  nextflow.cli.CmdRun - Launching `../main.nf` [Test RNA Run: 1512731087] - revision: 133563c128
  4. Dec-08 12:07:31.427 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /Users/philewels/GitHub/NGI-RNAseq/nextflow.config
  5. Dec-08 12:07:31.429 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/philewels/GitHub/NGI-RNAseq/nextflow.config
  6. Dec-08 12:07:31.794 [main] DEBUG nextflow.config.ConfigBuilder - Setting config profile: 'docker'
  7. Dec-08 12:07:31.953 [main] ERROR nextflow.cli.Launcher - Unable to parse config file: '/Users/philewels/GitHub/NGI-RNAseq/nextflow.config'
  8.  
  9.   Compile failed for sources FixedSetSources[name='/groovy/script/ScriptDF5F87B03A3555376BEDA7CE7D5F7998/_nf_config_9c78e99c']. Cause: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
  10.   /groovy/script/ScriptDF5F87B03A3555376BEDA7CE7D5F7998/_nf_config_9c78e99c: 91: unable to resolve class MemoryUnit
  11.    @ line 91, column 22.
  12.          if(obj.compareTo(params.max_memory as MemoryUnit) == 1)
  13.                           ^
  14.  
  15.   /groovy/script/ScriptDF5F87B03A3555376BEDA7CE7D5F7998/_nf_config_9c78e99c: 96: unable to resolve class TimeUnit
  16.    @ line 96, column 22.
  17.          if(obj.compareTo(params.max_time as TimeUnit) == 1)
  18.                           ^
  19.  
  20.   2 errors
  21.  
  22. ch.grengine.except.CompileException: Compile failed for sources FixedSetSources[name='/groovy/script/ScriptDF5F87B03A3555376BEDA7CE7D5F7998/_nf_config_9c78e99c']. Cause: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
  23. /groovy/script/ScriptDF5F87B03A3555376BEDA7CE7D5F7998/_nf_config_9c78e99c: 91: unable to resolve class MemoryUnit
  24.  @ line 91, column 22.
  25.        if(obj.compareTo(params.max_memory as MemoryUnit) == 1)
  26.                         ^
  27.  
  28. /groovy/script/ScriptDF5F87B03A3555376BEDA7CE7D5F7998/_nf_config_9c78e99c: 96: unable to resolve class TimeUnit
  29.  @ line 96, column 22.
  30.        if(obj.compareTo(params.max_time as TimeUnit) == 1)
  31.                         ^
  32.  
  33. 2 errors
  34.  
  35.     at ch.grengine.code.groovy.DefaultGroovyCompiler.compile(DefaultGroovyCompiler.java:182)
  36.     at ch.grengine.load.DefaultTopCodeCache.getUpToDateCode(DefaultTopCodeCache.java:77)
  37.     at ch.grengine.load.LayeredClassLoader.loadMainClass(LayeredClassLoader.java:165)
  38.     at ch.grengine.engine.LayeredEngine.loadMainClass(LayeredEngine.java:188)
  39.     at ch.grengine.Grengine.loadMainClass(Grengine.java:652)
  40.     at ch.grengine.BaseGrengine.load(BaseGrengine.java:356)
  41.     at ch.grengine.BaseGrengine.load(BaseGrengine.java:264)
  42.     at ch.grengine.BaseGrengine$load.call(Unknown Source)
  43.     at nextflow.config.ComposedConfigSlurper.loadScript(ComposedConfigSlurper.groovy:178)
  44.     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  45.     at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
  46.     at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  47.     at java.lang.reflect.Method.invoke(Method.java:498)
  48.     at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:210)
  49.     at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:59)
  50.     at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
  51.     at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154)
  52.     at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
  53.     at nextflow.config.ComposedConfigSlurper.parse(ComposedConfigSlurper.groovy:253)
  54.     at nextflow.config.ComposedConfigSlurper$parse$5.call(Unknown Source)
  55.     at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
  56.     at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
  57.     at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
  58.     at nextflow.config.ConfigBuilder$_buildConfig0_closure7.doCall(ConfigBuilder.groovy:274)
  59.     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  60.     at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
  61.     at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  62.     at java.lang.reflect.Method.invoke(Method.java:498)
  63.     at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
  64.     at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
  65.     at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
  66.     at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
  67.     at groovy.lang.Closure.call(Closure.java:414)
  68.     at groovy.lang.Closure.call(Closure.java:430)
  69.     at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2040)
  70.     at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2025)
  71.     at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2066)
  72.     at org.codehaus.groovy.runtime.dgm$162.invoke(Unknown Source)
  73.     at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
  74.     at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
  75.     at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
  76.     at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
  77.     at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
  78.     at nextflow.config.ConfigBuilder.buildConfig0(ConfigBuilder.groovy:267)
  79.     at nextflow.config.ConfigBuilder$buildConfig0$2.callCurrent(Unknown Source)
  80.     at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
  81.     at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154)
  82.     at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:174)
  83.     at nextflow.config.ConfigBuilder.buildConfig(ConfigBuilder.groovy:234)
  84.     at nextflow.config.ConfigBuilder$buildConfig$1.callCurrent(Unknown Source)
  85.     at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
  86.     at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154)
  87.     at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
  88.     at nextflow.config.ConfigBuilder.build(ConfigBuilder.groovy:490)
  89.     at nextflow.cli.CmdRun.run(CmdRun.groovy:203)
  90.     at nextflow.cli.Launcher.run(Launcher.groovy:410)
  91.     at nextflow.cli.Launcher.main(Launcher.groovy:564)
  92. Caused by: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
  93. /groovy/script/ScriptDF5F87B03A3555376BEDA7CE7D5F7998/_nf_config_9c78e99c: 91: unable to resolve class MemoryUnit
  94.  @ line 91, column 22.
  95.        if(obj.compareTo(params.max_memory as MemoryUnit) == 1)
  96.                         ^
  97.  
  98. /groovy/script/ScriptDF5F87B03A3555376BEDA7CE7D5F7998/_nf_config_9c78e99c: 96: unable to resolve class TimeUnit
  99.  @ line 96, column 22.
  100.        if(obj.compareTo(params.max_time as TimeUnit) == 1)
  101.                         ^
  102.  
  103. 2 errors
  104.  
  105.     at org.codehaus.groovy.control.ErrorCollector.failIfErrors(ErrorCollector.java:310)
  106.     at org.codehaus.groovy.control.CompilationUnit.applyToSourceUnits(CompilationUnit.java:958)
  107.     at org.codehaus.groovy.control.CompilationUnit.doPhaseOperation(CompilationUnit.java:605)
  108.     at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:554)
  109.     at ch.grengine.code.groovy.DefaultGroovyCompiler.compile(DefaultGroovyCompiler.java:145)
  110.     ... 56 common frames omitted
Advertisement
Add Comment
Please, Sign In to add comment
Advertisement
Public Pastes
Advertisement
We use cookies for various purposes including analytics. By continuing to use Pastebin, you agree to our use of cookies as described in the Cookies Policy.  OK, I Understand
Not a member of Pastebin yet?
Sign Up, it unlocks many cool features!