Skip to content

Instantly share code, notes, and snippets.

@Galithil

Galithil/gist:3b51717cff980bca27da9b3d8d5737b9

Created November 11, 2016 10:54
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save Galithil/3b51717cff980bca27da9b3d8d5737b9 to your computer and use it in GitHub Desktop.
Save Galithil/3b51717cff980bca27da9b3d8d5737b9 to your computer and use it in GitHub Desktop.
Download ZIP
Raw
gistfile1.txt
ls
data my_config nextflow.config
(lims2db) [11:52:39] denismoreno@130-229-4-0-dhcp: nextflow full.nf -profile ngi_docker -c my_config --reads 'data/*R{1,2}.fastq.gz'
Expected a command, got full.nf -- Check the available commands and options and syntax with 'help'
(lims2db) [11:52:51] denismoreno@130-229-4-0-dhcp: nextflow ../NGI-RNAseq/main.nf -profile ngi_docker -c my_config --reads 'data/*R{1,2}.fastq.gz'
N E X T F L O W ~ version 0.22.3
Launching `../NGI-RNAseq/main.nf` [prickly_heyrovsky] - revision: 8ea6e6d1de
ERROR ~ No such variable: enabled
-- Check '.nextflow.log' file for details
(lims2db) [11:53:05] denismoreno@130-229-4-0-dhcp: ls
data my_config nextflow.config
(lims2db) [11:53:26] denismoreno@130-229-4-0-dhcp: cat nextflow.config
profiles {
standard {
includeConfig 'conf/uppmax.config'
}
ngi_docker {
includeConfig '../NGI-RNAseq/conf/docker.config'
}
ngi_amazon {
cloud {
imageId = 'ami-d6ce34b9'
instanceType = 't2.micro'
subnetId = 'subnet-021dd978'
}
}
}
(lims2db) [11:53:30] denismoreno@130-229-4-0-dhcp: cat ../NGI-RNAseq/conf/docker.config
/*
vim: syntax=groovy
-*- mode: groovy;-*-
* -------------------------------------------------
* Nextflow config file for UPPMAX (milou / irma)
* -------------------------------------------------
* Defines reference genomes, using iGenome paths
* Imported under the default 'standard' Nextflow
* profile in nextflow.config
*/
docker.enabled = true
process {
container = 'scilifelab/ngi-rnaseq'
executor = 'local'
cpus = 1
memory = '16 GB'
time = '48h'
}
params {
download_fasta = 'ftp://ftp.ensembl.org/pub/release-86/gtf/homo_sapiens/Homo_sapiens.GRCh37.86.gtf.gz'
download_gtf = 'ftp://ftp.ensembl.org/pub/release-86/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.86.dna.primary_assembly.fa.gz'
}
(lims2db) [11:53:37] denismoreno@130-229-4-0-dhcp: nextflow ../NGI-RNAseq/main.nf -profile ngi_docker -c my_config --reads 'data/*R{1,2}.fastq.gz'
N E X T F L O W ~ version 0.22.3
Launching `../NGI-RNAseq/main.nf` [nostalgic_bell] - revision: 8ea6e6d1de
ERROR ~ No such variable: enabled
-- Check '.nextflow.log' file for details
(lims2db) [11:53:57] denismoreno@130-229-4-0-dhcp: cat .nextflow.log
Nov-11 11:53:57.277 [main] DEBUG nextflow.cli.Launcher - $> /usr/local/bin/nextflow ../NGI-RNAseq/main.nf -profile ngi_docker -c my_config --reads data/*R{1,2}.fastq.gz
Nov-11 11:53:57.351 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.22.3
Nov-11 11:53:57.364 [main] INFO nextflow.cli.CmdRun - Launching `../NGI-RNAseq/main.nf` [nostalgic_bell] - revision: 8ea6e6d1de
Nov-11 11:53:57.372 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /Users/denismoreno/Documents/NGI-RNAseq/nextflow.config
Nov-11 11:53:57.372 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: nextflow.config
Nov-11 11:53:57.373 [main] DEBUG nextflow.config.ConfigBuilder - User config file: my_config
Nov-11 11:53:57.375 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/denismoreno/Documents/NGI-RNAseq/nextflow.config
Nov-11 11:53:57.375 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/denismoreno/Documents/mytest/nextflow.config
Nov-11 11:53:57.375 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/denismoreno/Documents/mytest/my_config
Nov-11 11:53:57.611 [main] DEBUG nextflow.config.ConfigBuilder - Setting config profile: 'ngi_docker'
Nov-11 11:53:57.719 [main] ERROR nextflow.cli.Launcher - Unable to parse config file: '/Users/denismoreno/Documents/NGI-RNAseq/nextflow.config'
No such property: enabled for class: docker
groovy.lang.MissingPropertyException: No such property: enabled for class: docker
at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.unwrap(ScriptBytecodeAdapter.java:53)
at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.setProperty(ScriptBytecodeAdapter.java:486)
at docker.run(docker.config:12)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1215)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1082)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
at groovy.lang.Closure.call(Closure.java:414)
at groovy.lang.Closure.call(Closure.java:408)
at java_util_concurrent_Callable$call.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
at nextflow.config.ComposedConfigScript.includeConfig(ComposedConfigScript.groovy:106)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:384)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
at _nf_config_81933f62$_run_closure1$_closure3.doCall(_nf_config_81933f62:20)
at _nf_config_81933f62$_run_closure1$_closure3.doCall(_nf_config_81933f62)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
at nextflow.config.ComposedConfigSlurper$_parse_closure5.doCall(ComposedConfigSlurper.groovy:328)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaMethod.invoke(ClosureMetaMethod.java:84)
at groovy.lang.ExpandoMetaClass.invokeMethod(ExpandoMetaClass.java:1123)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:812)
at groovy.lang.DelegatingMetaClass.invokeMethod(DelegatingMetaClass.java:144)
at groovy.lang.GroovyObjectSupport.invokeMethod(GroovyObjectSupport.java:46)
at groovy.lang.Script.invokeMethod(Script.java:80)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:430)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:369)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
at _nf_config_81933f62$_run_closure1.doCall(_nf_config_81933f62:19)
at _nf_config_81933f62$_run_closure1.doCall(_nf_config_81933f62)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
at nextflow.config.ComposedConfigSlurper$_parse_closure5.doCall(ComposedConfigSlurper.groovy:310)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaMethod.invoke(ClosureMetaMethod.java:84)
at groovy.lang.ExpandoMetaClass.invokeMethod(ExpandoMetaClass.java:1123)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
at groovy.lang.DelegatingMetaClass.invokeMethod(DelegatingMetaClass.java:151)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
at _nf_config_81933f62.run(_nf_config_81933f62:13)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at org.codehaus.groovy.reflection.CachedMethod$invoke.call(Unknown Source)
at nextflow.config.ComposedConfigSlurper$_parse_closure5.doCall(ComposedConfigSlurper.groovy:356)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaMethod.invoke(ClosureMetaMethod.java:84)
at groovy.lang.ExpandoMetaClass.invokeMethod(ExpandoMetaClass.java:1123)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
at groovy.lang.DelegatingMetaClass.invokeMethod(DelegatingMetaClass.java:151)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:57)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
at nextflow.config.ComposedConfigSlurper.parse(ComposedConfigSlurper.groovy:384)
at nextflow.config.ComposedConfigSlurper$parse$1.callCurrent(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:174)
at nextflow.config.ComposedConfigSlurper.parse(ComposedConfigSlurper.groovy:253)
at nextflow.config.ComposedConfigSlurper$parse$5.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at nextflow.config.ConfigBuilder$_buildConfig0_closure7.doCall(ConfigBuilder.groovy:274)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
at groovy.lang.Closure.call(Closure.java:414)
at groovy.lang.Closure.call(Closure.java:430)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2030)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2015)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2056)
at org.codehaus.groovy.runtime.dgm$162.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at nextflow.config.ConfigBuilder.buildConfig0(ConfigBuilder.groovy:267)
at nextflow.config.ConfigBuilder$buildConfig0$2.callCurrent(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:174)
at nextflow.config.ConfigBuilder.buildConfig(ConfigBuilder.groovy:234)
at nextflow.config.ConfigBuilder$buildConfig$1.callCurrent(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
at nextflow.config.ConfigBuilder.build(ConfigBuilder.groovy:474)
at nextflow.cli.CmdRun.run(CmdRun.groovy:184)
at nextflow.cli.Launcher.run(Launcher.groovy:406)
at nextflow.cli.Launcher.main(Launcher.groovy:554)
@pditommaso
Copy link

not sure, but can you try to renamed docker.config to a different name eg. docker0.config

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment