java.lang.RuntimeException: Unable to parse clonotype string [...] for VDJtools input type: toIndex = 7

[jmelero611]

Hi there!

I have been dealing with this error, but I have no idea what is it and how to solve it. First I thought it was because the sequence was too short (less than 7), but it actually happens in also larger sequences.

Any idea about what is causing the error and how to solve it?

Thank you very much for your help!

Here I leave the log:

[Mon May 31 11:28:06 CEST 2021 BEGIN] [Script] CalcBasicStats [CommandLine] executing vdjtools-1.2.1.jar CalcBasicStats -m metadata.txt output [Message] java.lang.RuntimeException: Unable to parse clonotype string 88 0.0003630183324257875 TGTGCCAGCGAGGATCTGAGAAAT CASEDLRN TRBV12-2+TRBV13-2 for VDJtools input type: toIndex = 7 [StackTrace-Short] com.antigenomics.vdjtools.io.parser.ClonotypeStreamParser.parse(ClonotypeStreamParser.groovy:189) com.antigenomics.vdjtools.io.parser.ClonotypeStreamParser$_iterator_closure8.doCall(ClonotypeStreamParser.groovy:249) com.antigenomics.vdjtools.io.parser.ClonotypeStreamParser$_iterator_closure8.doCall(ClonotypeStreamParser.groovy) com.antigenomics.vdjtools.sample.Sample.fromInputStream(Sample.java:174) com.antigenomics.vdjtools.sample.Sample$fromInputStream.call(Unknown Source) com.antigenomics.vdjtools.io.SampleStreamConnection._load(SampleStreamConnection.groovy:128) com.antigenomics.vdjtools.io.SampleStreamConnection.getSample(SampleStreamConnection.groovy:139) com.antigenomics.vdjtools.sample.SampleCollection$_iterator_closure6.doCall(SampleCollection.groovy:320) com.antigenomics.vdjtools.sample.SampleCollection$_iterator_closure6.doCall(SampleCollection.groovy) com.antigenomics.vdjtools.basic.CalcBasicStats$_run_closure1.doCall(CalcBasicStats.groovy:102) com.antigenomics.vdjtools.basic.CalcBasicStats.run(CalcBasicStats.groovy:93) com.antigenomics.vdjtools.basic.CalcBasicStats$run.call(Unknown Source) com.antigenomics.vdjtools.misc.ExecUtil.run(ExecUtil.groovy:94) com.antigenomics.vdjtools.misc.ExecUtil$run.call(Unknown Source) com.antigenomics.vdjtools.VdjTools.run(VdjTools.groovy:226) com.antigenomics.vdjtools.VdjTools.main(VdjTools.groovy) [StackTrace-Full] java.lang.RuntimeException: Unable to parse clonotype string 88 0.0003630183324257875 TGTGCCAGCGAGGATCTGAGAAAT CASEDLRN TRBV12-2+TRBV13-2 for VDJtools input type: toIndex = 7 at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:59) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:238) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:258) at com.antigenomics.vdjtools.io.parser.ClonotypeStreamParser.parse(ClonotypeStreamParser.groovy:189) at jdk.internal.reflect.GeneratedMethodAccessor15.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:104) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:326) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:352) at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:68) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:169) at com.antigenomics.vdjtools.io.parser.ClonotypeStreamParser$_iterator_closure8.doCall(ClonotypeStreamParser.groovy:249) at com.antigenomics.vdjtools.io.parser.ClonotypeStreamParser$_iterator_closure8.doCall(ClonotypeStreamParser.groovy) at jdk.internal.reflect.GeneratedMethodAccessor14.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:104) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:326) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:264) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1041) at groovy.lang.Closure.call(Closure.java:421) at org.codehaus.groovy.runtime.ConvertedMap.invokeCustom(ConvertedMap.java:54) at org.codehaus.groovy.runtime.ConversionHandler.invoke(ConversionHandler.java:124) at com.sun.proxy.$Proxy6.next(Unknown Source) at com.antigenomics.vdjtools.sample.Sample.fromInputStream(Sample.java:174) at com.antigenomics.vdjtools.sample.Sample$fromInputStream.call(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116) at com.antigenomics.vdjtools.io.SampleStreamConnection._load(SampleStreamConnection.groovy:128) at com.antigenomics.vdjtools.io.SampleStreamConnection.getSample(SampleStreamConnection.groovy:139) at com.antigenomics.vdjtools.sample.SampleCollection$_iterator_closure6.doCall(SampleCollection.groovy:320) at com.antigenomics.vdjtools.sample.SampleCollection$_iterator_closure6.doCall(SampleCollection.groovy) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:104) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:326) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:264) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1041) at groovy.lang.Closure.call(Closure.java:421) at org.codehaus.groovy.runtime.ConvertedMap.invokeCustom(ConvertedMap.java:54) at org.codehaus.groovy.runtime.ConversionHandler.invoke(ConversionHandler.java:124) at com.sun.proxy.$Proxy6.next(Unknown Source) at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2294) at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2280) at org.codehaus.groovy.runtime.dgm$181.invoke(Unknown Source) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoMetaMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:223) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.call(PogoMetaMethodSite.java:70) 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 com.antigenomics.vdjtools.basic.CalcBasicStats$_run_closure1.doCall(CalcBasicStats.groovy:102) 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:104) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:326) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:264) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1041) at groovy.lang.Closure.call(Closure.java:421) at groovy.lang.Closure.call(Closure.java:437) at org.codehaus.groovy.runtime.IOGroovyMethods.withWriter(IOGroovyMethods.java:1139) at org.codehaus.groovy.runtime.ResourceGroovyMethods.withPrintWriter(ResourceGroovyMethods.java:2115) at org.codehaus.groovy.runtime.dgm$1073.invoke(Unknown Source) at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:246) at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:55) 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 com.antigenomics.vdjtools.basic.CalcBasicStats.run(CalcBasicStats.groovy:93) at com.antigenomics.vdjtools.basic.CalcBasicStats$run.call(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:120) at com.antigenomics.vdjtools.misc.ExecUtil.run(ExecUtil.groovy:94) at com.antigenomics.vdjtools.misc.ExecUtil$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 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:104) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:326) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1235) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1041) at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:1018) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:1001) at org.codehaus.groovy.runtime.InvokerHelper.runScript(InvokerHelper.java:423) 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.IndexOutOfBoundsException: toIndex = 7 at java.base/java.util.AbstractList.subListRangeCheck(AbstractList.java:507) at java.base/java.util.AbstractList.subList(AbstractList.java:497) at org.codehaus.groovy.runtime.DefaultGroovyMethods.getAt(DefaultGroovyMethods.java:7540) at org.codehaus.groovy.runtime.DefaultGroovyMethods.getAt(DefaultGroovyMethods.java:7778) at org.codehaus.groovy.runtime.dgm$320.invoke(Unknown Source) at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:246) at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:55) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:128) at com.antigenomics.vdjtools.io.parser.BaseParser.innerParse(BaseParser.groovy:73) at com.antigenomics.vdjtools.io.parser.ClonotypeStreamParser.parse(ClonotypeStreamParser.groovy:159) ... 95 more [END]

[f6v]

@jmelero611 have you ever figured it out?