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Sorry to bother you, i run the code as following, Want to know how I should solve it? Thanks! the metadeata.txt with three cols: file_name sample_id and group.
java -Xmx4G -jar /usr/share/java/vdjtools-1.2.1.jar Convert -S mixcr -m /home/dell/PRJEBxx/mixcr/IGH/metadata.txt output_prefix
Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/commons/cli/ParseException
at java.lang.Class.getDeclaredConstructors0(Native Method)
at java.lang.Class.privateGetDeclaredConstructors(Class.java:2671)
at java.lang.Class.getDeclaredConstructors(Class.java:2020)
at org.codehaus.groovy.reflection.CachedClass$2$1.run(CachedClass.java:88)
at java.security.AccessController.doPrivileged(Native Method)
at org.codehaus.groovy.reflection.CachedClass$2.initValue(CachedClass.java:86)
at org.codehaus.groovy.reflection.CachedClass$2.initValue(CachedClass.java:81)
at org.codehaus.groovy.util.LazyReference.getLocked(LazyReference.java:50)
at org.codehaus.groovy.util.LazyReference.get(LazyReference.java:37)
at org.codehaus.groovy.reflection.CachedClass.getConstructors(CachedClass.java:311)
at groovy.lang.MetaClassImpl.(MetaClassImpl.java:233)
at groovy.lang.MetaClassImpl.(MetaClassImpl.java:243)
at groovy.lang.MetaClassRegistry$MetaClassCreationHandle.createNormalMetaClass(MetaClassRegistry.java:171)
at groovy.lang.MetaClassRegistry$MetaClassCreationHandle.createWithCustomLookup(MetaClassRegistry.java:161)
at groovy.lang.MetaClassRegistry$MetaClassCreationHandle.create(MetaClassRegistry.java:144)
at org.codehaus.groovy.reflection.ClassInfo.getMetaClassUnderLock(ClassInfo.java:288)
at org.codehaus.groovy.reflection.ClassInfo.getMetaClass(ClassInfo.java:331)
at org.codehaus.groovy.runtime.metaclass.MetaClassRegistryImpl.getMetaClass(MetaClassRegistryImpl.java:277)
at org.codehaus.groovy.runtime.InvokerHelper.getMetaClass(InvokerHelper.java:905)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.createCallConstructorSite(CallSiteArray.java:86)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:59)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:238)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:250)
at com.antigenomics.vdjtools.misc.Convert.run(Convert.groovy:35)
at com.antigenomics.vdjtools.misc.Convert$run.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:120)
at com.antigenomics.vdjtools.misc.ExecUtil.run(ExecUtil.groovy:94)
at com.antigenomics.vdjtools.misc.ExecUtil$run.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 com.antigenomics.vdjtools.VdjTools.run(VdjTools.groovy:226)
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:104)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1226)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
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$runScript.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:136)
at com.antigenomics.vdjtools.VdjTools.main(VdjTools.groovy)
Caused by: java.lang.ClassNotFoundException: org.apache.commons.cli.ParseException
at java.net.URLClassLoader.findClass(URLClassLoader.java:387)
at java.lang.ClassLoader.loadClass(ClassLoader.java:418)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
at java.lang.ClassLoader.loadClass(ClassLoader.java:351)
... 50 more
The text was updated successfully, but these errors were encountered:
Sorry to bother you, i run the code as following, Want to know how I should solve it? Thanks! the metadeata.txt with three cols: file_name sample_id and group.
java -Xmx4G -jar /usr/share/java/vdjtools-1.2.1.jar Convert -S mixcr -m /home/dell/PRJEBxx/mixcr/IGH/metadata.txt output_prefix
Executing com.antigenomics.vdjtools.misc.Convert -S mixcr -m /home/dell/PRJEBxx/mixcr/IGH/metadata.txt output_prefix
Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/commons/cli/ParseException
at java.lang.Class.getDeclaredConstructors0(Native Method)
at java.lang.Class.privateGetDeclaredConstructors(Class.java:2671)
at java.lang.Class.getDeclaredConstructors(Class.java:2020)
at org.codehaus.groovy.reflection.CachedClass$2$1.run(CachedClass.java:88)
at java.security.AccessController.doPrivileged(Native Method)
at org.codehaus.groovy.reflection.CachedClass$2.initValue(CachedClass.java:86)
at org.codehaus.groovy.reflection.CachedClass$2.initValue(CachedClass.java:81)
at org.codehaus.groovy.util.LazyReference.getLocked(LazyReference.java:50)
at org.codehaus.groovy.util.LazyReference.get(LazyReference.java:37)
at org.codehaus.groovy.reflection.CachedClass.getConstructors(CachedClass.java:311)
at groovy.lang.MetaClassImpl.(MetaClassImpl.java:233)
at groovy.lang.MetaClassImpl.(MetaClassImpl.java:243)
at groovy.lang.MetaClassRegistry$MetaClassCreationHandle.createNormalMetaClass(MetaClassRegistry.java:171)
at groovy.lang.MetaClassRegistry$MetaClassCreationHandle.createWithCustomLookup(MetaClassRegistry.java:161)
at groovy.lang.MetaClassRegistry$MetaClassCreationHandle.create(MetaClassRegistry.java:144)
at org.codehaus.groovy.reflection.ClassInfo.getMetaClassUnderLock(ClassInfo.java:288)
at org.codehaus.groovy.reflection.ClassInfo.getMetaClass(ClassInfo.java:331)
at org.codehaus.groovy.runtime.metaclass.MetaClassRegistryImpl.getMetaClass(MetaClassRegistryImpl.java:277)
at org.codehaus.groovy.runtime.InvokerHelper.getMetaClass(InvokerHelper.java:905)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.createCallConstructorSite(CallSiteArray.java:86)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:59)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:238)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:250)
at com.antigenomics.vdjtools.misc.Convert.run(Convert.groovy:35)
at com.antigenomics.vdjtools.misc.Convert$run.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:120)
at com.antigenomics.vdjtools.misc.ExecUtil.run(ExecUtil.groovy:94)
at com.antigenomics.vdjtools.misc.ExecUtil$run.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 com.antigenomics.vdjtools.VdjTools.run(VdjTools.groovy:226)
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:104)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1226)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
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$runScript.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:136)
at com.antigenomics.vdjtools.VdjTools.main(VdjTools.groovy)
Caused by: java.lang.ClassNotFoundException: org.apache.commons.cli.ParseException
at java.net.URLClassLoader.findClass(URLClassLoader.java:387)
at java.lang.ClassLoader.loadClass(ClassLoader.java:418)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
at java.lang.ClassLoader.loadClass(ClassLoader.java:351)
... 50 more
The text was updated successfully, but these errors were encountered: