Exception in thread "Thread-integer1" java.lang.IllegalArgumentException: multiply() should be called with a number of 0 or greater not: -integer2

[LukeHebert]

Executing the following MiGMAP command

/foo/jdk1.8.0_311/bin/java \
-jar /foo/MiGMAP/migmap-1.0.3/migmap-1.0.3.jar \
--blast-dir /foo/igblast_1.4.0_binaries/ \
--custom-database /foo/MiGMAP/MiGMAP_reference_DB2_refs_humanized.txt \
--all-alleles \
--allow-incomplete \
--allow-no-cdr3 \
--allow-noncanonical \
--details fr1nt,cdr1nt,fr2nt,cdr2nt,fr3nt,fr4nt,contignt,fr1aa,cdr1aa,fr2aa,cdr2aa,fr3aa,fr4aa,contigaa \
-q 2 \
--report bar_mapping_report.txt \
--unmapped bar_unmapped_reads.fastq \
-R IGH,IGK,IGL \
-S human \
--by-read \
bar.assembled.fastq \
bar_database.txt

produces a series of similar java thread exception messages that look like these two (for example):

Exception in thread "Thread-118" java.lang.IllegalArgumentException: multiply() should be called with a number of 0 or greater not: -170
        at org.codehaus.groovy.runtime.StringGroovyMethods.multiply(StringGroovyMethods.java:2057)
        at com.antigenomics.migmap.mapping.ReadMappingDetailsProvider$ReadMappingDetails.getFr3nt(ReadMappingDetailsProvider.groovy:145)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
        at groovy.lang.MetaClassImpl.getProperty(MetaClassImpl.java:1850)
        at groovy.lang.MetaClassImpl.getProperty(MetaClassImpl.java:3758)
        at com.antigenomics.migmap.mapping.ReadMappingDetailsProvider$ReadMappingDetails.getProperty(ReadMappingDetailsProvider.groovy)
        at org.codehaus.groovy.runtime.InvokerHelper.getProperty(InvokerHelper.java:174)
        at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.getProperty(ScriptBytecodeAdapter.java:456)
        at com.antigenomics.migmap.mapping.ReadMappingDetailsProvider$_getDetailsString_closure3.doCall(ReadMappingDetailsProvider.groovy:65)
        at sun.reflect.GeneratedMethodAccessor26.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.collect(DefaultGroovyMethods.java:3202)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.collect(DefaultGroovyMethods.java:3172)
        at org.codehaus.groovy.runtime.dgm$67.invoke(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$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.mapping.ReadMappingDetailsProvider.getDetailsString(ReadMappingDetailsProvider.groovy:65)
        at com.antigenomics.migmap.io.ReadMappingOutput.put(ReadMappingOutput.groovy:40)
        at com.antigenomics.migmap.io.ReadMappingOutput.put(ReadMappingOutput.groovy)
        at com.antigenomics.migmap.pipeline.Pipeline$2.run(Pipeline.groovy:86)
        at java.lang.Thread.run(Thread.java:748)
Exception in thread "Thread-67" java.lang.IllegalArgumentException: multiply() should be called with a number of 0 or greater not: -170
        at org.codehaus.groovy.runtime.StringGroovyMethods.multiply(StringGroovyMethods.java:2057)
        at com.antigenomics.migmap.mapping.ReadMappingDetailsProvider$ReadMappingDetails.getFr3nt(ReadMappingDetailsProvider.groovy:145)
        at sun.reflect.GeneratedMethodAccessor55.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 groovy.lang.MetaClassImpl.getProperty(MetaClassImpl.java:1850)
        at groovy.lang.MetaClassImpl.getProperty(MetaClassImpl.java:3758)
        at com.antigenomics.migmap.mapping.ReadMappingDetailsProvider$ReadMappingDetails.getProperty(ReadMappingDetailsProvider.groovy)
        at org.codehaus.groovy.runtime.InvokerHelper.getProperty(InvokerHelper.java:174)
        at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.getProperty(ScriptBytecodeAdapter.java:456)
        at com.antigenomics.migmap.mapping.ReadMappingDetailsProvider$_getDetailsString_closure3.doCall(ReadMappingDetailsProvider.groovy:65)
        at sun.reflect.GeneratedMethodAccessor26.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.collect(DefaultGroovyMethods.java:3202)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.collect(DefaultGroovyMethods.java:3172)
        at org.codehaus.groovy.runtime.dgm$67.invoke(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$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.mapping.ReadMappingDetailsProvider.getDetailsString(ReadMappingDetailsProvider.groovy:65)
        at com.antigenomics.migmap.io.ReadMappingOutput.put(ReadMappingOutput.groovy:40)
        at com.antigenomics.migmap.io.ReadMappingOutput.put(ReadMappingOutput.groovy)
        at com.antigenomics.migmap.pipeline.Pipeline$2.run(Pipeline.groovy:86)
        at java.lang.Thread.run(Thread.java:748)

Using the "--by-read" argument produces multiple thread exceptions. Without the "--by-read" argument, only one exception is thrown after MiGMAP finishes mapping and writing the annotated output file. So far, I am unsure if the multiple thread exceptions generated using the "--by-read" argument are detrimental to writing all output data or not.