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I am running migmap on bulk RNASeq data from tumour biopsies in a conda environment and I have encountered the following error with com.antigenomics.migmap.Correct during post-processing.
When I run com.antigenomics.migmap.Correct on the output of com.antigenomics.migmap.MergeContigs I get a string indexing error for all but one of my samples (detailed below). The error seems to be related to mutations whose position exceeds the number of nucleotides in contigNt.
Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: 269
at java.lang.String.substring(String.java:1963)
at org.codehaus.groovy.runtime.StringGroovyMethods.getAt(StringGroovyMethods.java:1463)
at org.codehaus.groovy.runtime.dgm$1089.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at com.antigenomics.migmap.Correct$_run_closure3$_closure22.doCall(Correct.groovy:138)
at sun.reflect.GeneratedMethodAccessor9.invoke(Unknown Source)
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:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.BooleanReturningMethodInvoker.invoke(BooleanReturningMethodInvoker.java:51)
at org.codehaus.groovy.runtime.callsite.BooleanClosureWrapper.call(BooleanClosureWrapper.java:53)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.findAll(DefaultGroovyMethods.java:4331)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.findAll(DefaultGroovyMethods.java:4203)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.findAll(DefaultGroovyMethods.java:4175)
at org.codehaus.groovy.runtime.dgm$206.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at com.antigenomics.migmap.Correct$_run_closure3.doCall(Correct.groovy:136)
at sun.reflect.GeneratedMethodAccessor12.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:133)
at com.antigenomics.migmap.Correct$_run_closure4$_closure23$_closure24.doCall(Correct.groovy:154)
at sun.reflect.GeneratedMethodAccessor10.invoke(Unknown Source)
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:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
at groovy.lang.Closure.call(Closure.java:414)
at groovy.lang.Closure.call(Closure.java:430)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2040)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2025)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2066)
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.AbstractCallSite.call(AbstractCallSite.java:125)
at com.antigenomics.migmap.Correct$_run_closure4$_closure23.doCall(Correct.groovy:150)
at sun.reflect.GeneratedMethodAccessor14.invoke(Unknown Source)
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:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
at groovy.lang.Closure.call(Closure.java:414)
at groovy.lang.Closure.call(Closure.java:430)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2040)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2025)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2066)
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.AbstractCallSite.call(AbstractCallSite.java:125)
at com.antigenomics.migmap.Correct$_run_closure4.doCall(Correct.groovy:143)
at sun.reflect.GeneratedMethodAccessor16.invoke(Unknown Source)
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:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
at groovy.lang.Closure.call(Closure.java:414)
at groovy.lang.Closure.call(Closure.java:430)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2040)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2025)
at org.codehaus.groovy.runtime.dgm$159.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$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:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at com.antigenomics.migmap.Correct.run(Correct.groovy:142)
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:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1213)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:925)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:908)
at org.codehaus.groovy.runtime.InvokerHelper.runScript(InvokerHelper.java:412)
at org.codehaus.groovy.runtime.InvokerHelper$runScript.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:133)
at com.antigenomics.migmap.Correct.main(Correct.groovy)
This is a possible duplicate of #46 but since there are no responses to that issue, any help that you could provide would be greatly appreciated.
The text was updated successfully, but these errors were encountered:
I am running migmap on bulk RNASeq data from tumour biopsies in a conda environment and I have encountered the following error with
com.antigenomics.migmap.Correctduring post-processing.When I run
com.antigenomics.migmap.Correcton the output ofcom.antigenomics.migmap.MergeContigsI get a string indexing error for all but one of my samples (detailed below). The error seems to be related to mutations whose position exceeds the number of nucleotides in contigNt.This is a possible duplicate of #46 but since there are no responses to that issue, any help that you could provide would be greatly appreciated.
The text was updated successfully, but these errors were encountered: