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My guess is there is a syntax error in this config file: |
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Hi @452jiajia. I recently ran into exactly this same error. As @bentsherman said, it was an error in my nextflow.config file. In my case, I had failed to encapsulate a path in single quotes:
I think the slash character was being interpreted as a division operation. As soon as I wrapped the path in quotes (see below) the error went away.
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Hi guys, I'm having some problems running nextflow, when I'm using nextflow run nf-core/rnaeq, the above error occurs, please do you all have a similar experience, here is my nextflow.log
Mar-27 08:24:19.477 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/rnaseq
Mar-27 08:24:19.594 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.10.1
Mar-27 08:24:19.631 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/gaojb/.nextflow/plugins; core-plugins: nf-amazon@2.1.4,nf-azure@1.3.3,nf-cloudcache@0.3.0,nf-codecommit@0.1.5,nf-console@1.0.6,nf-ga4gh@1.1.0,nf-google@1.8.3,nf-tower@1.6.3,nf-wave@1.0.1
Mar-27 08:24:19.647 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Mar-27 08:24:19.649 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Mar-27 08:24:19.654 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Mar-27 08:24:19.671 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Mar-27 08:24:19.693 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/gaojb/.nextflow/scm
Mar-27 08:24:21.297 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/gaojb/.nextflow/assets/nf-core/rnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/rnaseq.git
Mar-27 08:24:21.326 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Mar-27 08:24:21.338 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/gaojb/.nextflow/assets/nf-core/rnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/rnaseq.git
Mar-27 08:24:23.217 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/gaojb/.nextflow/assets/nf-core/rnaseq/nextflow.config
Mar-27 08:24:23.217 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /mnt/gaojb/software/easel/nextflow.config
Mar-27 08:24:23.218 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/gaojb/.nextflow/assets/nf-core/rnaseq/nextflow.config
Mar-27 08:24:23.218 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /mnt/gaojb/software/easel/nextflow.config
Mar-27 08:24:23.230 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: standard
Mar-27 08:24:26.489 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: standard
Mar-27 08:24:26.721 [main] ERROR nextflow.cli.Launcher - Unable to parse config file: '/mnt/gaojb/software/easel/nextflow.config'
No signature of method: groovy.util.ConfigObject.div() is applicable for argument types: (ConfigObject) values: [[:]]
Possible solutions: min(groovy.lang.Closure), is(java.lang.Object), wait(), size(), any(), dump()
groovy.lang.MissingMethodException: No signature of method: groovy.util.ConfigObject.div() is applicable for argument types: (ConfigObject) values: [[:]]
Possible solutions: min(groovy.lang.Closure), is(java.lang.Object), wait(), size(), any(), dump()
at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.unwrap(ScriptBytecodeAdapter.java:70)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:50)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
at _nf_config_820f7db2$_run_closure1.doCall(_nf_config_820f7db2:81)
at _nf_config_820f7db2$_run_closure1.doCall(_nf_config_820f7db2)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:38)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:53)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:130)
at nextflow.config.ConfigParser$_parse_closure5.doCall(ConfigParser.groovy:427)
at jdk.internal.reflect.GeneratedMethodAccessor8.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaMethod.invoke(ClosureMetaMethod.java:83)
at groovy.lang.ExpandoMetaClass.invokeMethod(ExpandoMetaClass.java:1118)
at groovy.lang.DelegatingMetaClass.invokeMethod(DelegatingMetaClass.java:226)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:61)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:185)
at _nf_config_820f7db2.run(_nf_config_820f7db2:8)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at org.codehaus.groovy.reflection.CachedMethod$invoke.call(Unknown Source)
at nextflow.config.ConfigParser$_parse_closure5.doCall(ConfigParser.groovy:448)
at jdk.internal.reflect.GeneratedMethodAccessor8.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaMethod.invoke(ClosureMetaMethod.java:83)
at groovy.lang.ExpandoMetaClass.invokeMethod(ExpandoMetaClass.java:1118)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
at groovy.lang.DelegatingMetaClass.invokeMethod(DelegatingMetaClass.java:147)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:38)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:53)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:130)
at nextflow.config.ConfigParser.parse(ConfigParser.groovy:476)
at nextflow.config.ConfigParser$parse$0.callCurrent(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at nextflow.config.ConfigParser$parse$0.callCurrent(Unknown Source)
at nextflow.config.ConfigParser.parse(ConfigParser.groovy:303)
at nextflow.config.ConfigParser$parse$5.call(Unknown Source)
at nextflow.config.ConfigBuilder.parse0(ConfigBuilder.groovy:434)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:48)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:189)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:57)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:194)
at nextflow.config.ConfigBuilder.merge0(ConfigBuilder.groovy:420)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:48)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:189)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:57)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:203)
at nextflow.config.ConfigBuilder.buildConfig0(ConfigBuilder.groovy:370)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:48)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:189)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:57)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:194)
at nextflow.config.ConfigBuilder.buildGivenFiles(ConfigBuilder.groovy:315)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:48)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:189)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:57)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:185)
at nextflow.config.ConfigBuilder.buildConfigObject(ConfigBuilder.groovy:806)
at nextflow.config.ConfigBuilder.build(ConfigBuilder.groovy:819)
at nextflow.cli.CmdRun.run(CmdRun.groovy:324)
at nextflow.cli.Launcher.run(Launcher.groovy:500)
at nextflow.cli.Launcher.main(Launcher.groovy:672)
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