search

oschwengers / asap

A scalable bacterial genome assembly, annotation and analysis pipeline
https://doi.org/10.1371/journal.pcbi.1007134
GNU General Public License v3.0
66 stars 18 forks source link

Groovy error at startup #27

Closed mtruglio closed 1 year ago

mtruglio commented 1 year ago

Hello, I installed ASAP following the directions in the manual, but when I try to execute the launcher, I get the error below. I am running Ubuntu 20.04, and I tried both OpenJDK v.8 and v.14. Do you know what this is about?

ps. The same happens if I try to start the docker container manually.

ASA³P:   /home/mtruglio/asap
DATA:    /home/work/pseudomonas_aeruginosa/asap
Scratch: /mnt/DataDrive/tmp
Exception in thread "main" groovy.lang.MissingPropertyException: No such property: fileName for class: bio.comp.jlu.asap.ASAP
        at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.unwrap(ScriptBytecodeAdapter.java:66)
        at org.codehaus.groovy.runtime.callsite.PogoGetPropertySite.getProperty(PogoGetPropertySite.java:51)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callGroovyObjectGetProperty(AbstractCallSite.java:310)
        at bio.comp.jlu.asap.ASAP$_checkConfig_closure7$_closure19$_closure20.doCall(ASAP.groovy:445)
        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:98)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:264)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1034)
        at groovy.lang.Closure.call(Closure.java:420)
        at groovy.lang.Closure.call(Closure.java:436)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2125)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2110)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2151)
        at org.codehaus.groovy.runtime.dgm$163.invoke(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$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:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:128)
        at bio.comp.jlu.asap.ASAP$_checkConfig_closure7$_closure19.doCall(ASAP.groovy:443)
        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:98)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:264)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1034)
        at groovy.lang.Closure.call(Closure.java:420)
        at groovy.lang.Closure.call(Closure.java:436)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2125)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2110)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2151)
        at org.codehaus.groovy.runtime.dgm$163.invoke(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$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:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:128)
        at bio.comp.jlu.asap.ASAP$_checkConfig_closure7.doCall(ASAP.groovy:434)
        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:98)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:264)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1034)
        at groovy.lang.Closure.call(Closure.java:420)
        at groovy.lang.Closure.call(Closure.java:436)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2125)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2110)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2151)
        at org.codehaus.groovy.runtime.dgm$163.invoke(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$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:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:128)
        at bio.comp.jlu.asap.ASAP.checkConfig(ASAP.groovy:403)
        at bio.comp.jlu.asap.ASAP$checkConfig.callCurrent(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:157)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:177)
        at bio.comp.jlu.asap.ASAP.run(ASAP.groovy:266)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:98)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1225)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1034)
        at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:947)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:930)
        at org.codehaus.groovy.runtime.InvokerHelper.runScript(InvokerHelper.java:428)
        at org.codehaus.groovy.runtime.InvokerHelper$runScript.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:136)
        at bio.comp.jlu.asap.ASAP.main(ASAP.groovy)
oschwengers commented 1 year ago

Hi, thanks for reaching out! Could you please provide some background on this: ASA³P version and the log file. I'll have a look at it.

mtruglio commented 1 year ago

Hi, I managed to find out what the problem was. Inside the "data" folder I was putting links to my fastq files, not the files themselves (I did not want to move or copy them, they're huge). I found out that ASAP does not like links, it wants the proper files. Maybe there's a way to fix this in the future? :)

Thanks anyway.

M

oschwengers commented 1 year ago

Yes, that could cause some issues, for instance using data in directories that are attached as Docker volumes. Best regards.