mikessh/migec

help running migec-1.2.1a

djoconnell opened this issue · 2 comments

djoconnell commented

I am great admirer of this work and also not well versed in programming, but I managed to get to the CdrBlastBatch step of my mouse TCR analysis when I run into problem.

It seems to get through some of the CdrBlast for the first sample because it creates a new folder "TSO_Well_92_R12.t3.cf.fastq.gz-cdrblast-6314a4a9-febf-48d1-a6ae-3fc821910c14" in the assemble directory.

Thank you very much and apologies if this is not the correct forum for contact help.

Best regards

[gmc6a-2ec:~/Desktop/TCRb_MIGDEC] dconnell% java -Xmx8G -jar migec-1.2.1a.jar CdrBlastBatch --sample-metadata 2015_06_18_Listeria_Metadata.txt checkout/ assemble/ cdrblast/
Jun 25, 2015 7:36:57 PM org.codehaus.groovy.runtime.m12n.MetaInfExtensionModule newModule
WARNING: Module [groovy-all] - Unable to load extension class [org.codehaus.groovy.runtime.NioGroovyMethods]
Executing com.milaboratory.migec.CdrBlastBatch --sample-metadata 2015_06_18_Listeria_Metadata.txt checkout/ assemble/ cdrblast/
[Thu Jun 25 19:36:58 EDT 2015 com.milaboratory.migec.CdrBlastBatch] Running CdrBlast for raw and assembled data..
Executing com.milaboratory.migec.CdrBlast --same-sample -R TRB -S MusMusculus -a -q 30" /Users/dconnell/Desktop/TCRb_MIGDEC/assemble/TSO_Well_92_R12.t3.cf.fastq.gz cdrblast/TSO_Well_92.asm.cdrblast.txt
[Thu Jun 25 19:36:58 EDT 2015 com.milaboratory.migec.CdrBlast] Loading TRB Variable and Joining segment data
[Thu Jun 25 19:36:58 EDT 2015 com.milaboratory.migec.CdrBlast] Generating BLAST database for TRB V
[Thu Jun 25 19:36:58 EDT 2015 com.milaboratory.migec.CdrBlast] Generating BLAST database for TRB J
Exception in thread "main" java.lang.UnsupportedClassVersionError: com/milaboratory/migec/dalign/SegmentSearcher : Unsupported major.minor version 51.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637)
at java.lang.ClassLoader.defineClass(ClassLoader.java:621)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at com.milaboratory.migec.CdrBlast.run(CdrBlast.groovy:299)
at com.milaboratory.migec.CdrBlast$run.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45)
at com.milaboratory.migec.CdrBlastBatch$run.call(Unknown Source)
at com.milaboratory.migec.Util.run(Util.groovy:36)
at com.milaboratory.migec.Util$run.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:108)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:120)
at com.milaboratory.migec.CdrBlastBatch$_run_closure8_closure14.doCall(CdrBlastBatch.groovy:298)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:90)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:233)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:272)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:909)
at groovy.lang.Closure.call(Closure.java:423)
at groovy.lang.Closure.call(Closure.java:439)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.callClosureForMapEntry(DefaultGroovyMethods.java:4242)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:1402)
at org.codehaus.groovy.runtime.dgm$151.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:271)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:53)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:108)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
at com.milaboratory.migec.CdrBlastBatch$_run_closure8.doCall(CdrBlastBatch.groovy:248)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:90)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:233)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:272)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:909)
at groovy.lang.Closure.call(Closure.java:423)
at groovy.lang.Closure.call(Closure.java:439)
at org.codehaus.groovy.runtime.IOGroovyMethods.withWriter(IOGroovyMethods.java:1134)
at org.codehaus.groovy.runtime.ResourceGroovyMethods.withPrintWriter(ResourceGroovyMethods.java:1877)
at org.codehaus.groovy.runtime.dgm$877.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:271)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:53)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:108)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
at com.milaboratory.migec.CdrBlastBatch.run(CdrBlastBatch.groovy:228)
at com.milaboratory.migec.CdrBlastBatch$run.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:108)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:112)
at com.milaboratory.migec.Util.run(Util.groovy:36)
at com.milaboratory.migec.Util$run.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:108)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:120)
at com.milaboratory.migec.Migec.run(Migec.groovy:103)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:90)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:233)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1085)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:909)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:901)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:884)
at org.codehaus.groovy.runtime.InvokerHelper.runScript(InvokerHelper.java:406)
at org.codehaus.groovy.runtime.InvokerHelper$runScript.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:108)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:120)
at com.milaboratory.migec.Migec.main(Migec.groovy)

mikessh commented

Hello!

Thanks for you feedback! The "Unsupported major.minor version 51.0" error generally comes from using wrong java version, see http://stackoverflow.com/questions/10382929/how-to-fix-unsupported-major-minor-version-51-0-error

Can you check the version of Java that you are using with java -version? I would recommend to install JRE 1.8 and see if it runs fine. Please let me know if the issue is resolved.

djoconnell commented

Thank you!

Works beautifully now. MIGEC calls clones from ~23% of my wells. I need to boost the RNA-seq library quality a bit more. Thank you again for your help and for creating the immune repertoires sequencing analysis pipelines.

Best regards,

Dan