vdjtools error

[qiangfan2022]

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