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- [2019/07/22 19:57:51 | FgBioMain | Info] TrimPrimers failed. Elapsed time: 0.04 minutes.
- Exception in thread "main" com.fulcrumgenomics.commons.reflect.ReflectionException: Could not build a 'int' from a string: : null
- sun.reflect.GeneratedConstructorAccessor7.newInstance(Unknown Source)
- sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
- java.lang.reflect.Constructor.newInstance(Constructor.java:423)
- com.fulcrumgenomics.commons.reflect.ReflectionUtil$.$anonfun$buildUnitFromString$5(ReflectionUtil.scala:398)
- scala.util.Try$.apply(Try.scala:213)
- com.fulcrumgenomics.commons.reflect.ReflectionUtil$.$anonfun$buildUnitFromString$1(ReflectionUtil.scala:394)
- scala.util.Try$.apply(Try.scala:213)
- com.fulcrumgenomics.commons.reflect.ReflectionUtil$.buildUnitFromString(ReflectionUtil.scala:370)
- com.fulcrumgenomics.commons.reflect.ReflectionUtil$.$anonfun$buildUnitOrOptionFromString$1(ReflectionUtil.scala:364)
- scala.util.Try$.apply(Try.scala:213)
- com.fulcrumgenomics.commons.reflect.ReflectionUtil$.buildUnitOrOptionFromString(ReflectionUtil.scala:363)
- com.fulcrumgenomics.commons.reflect.ReflectionUtil$.$anonfun$typedValueFromString$1(ReflectionUtil.scala:349)
- scala.util.Try$.apply(Try.scala:213)
- com.fulcrumgenomics.commons.reflect.ReflectionUtil$.typedValueFromString(ReflectionUtil.scala:315)
- com.fulcrumgenomics.commons.reflect.ReflectionUtil$.$anonfun$constructFromString$1(ReflectionUtil.scala:293)
- scala.util.Try$.apply(Try.scala:213)
- com.fulcrumgenomics.commons.reflect.ReflectionUtil$.constructFromString(ReflectionUtil.scala:287)
- com.fulcrumgenomics.commons.util.Row.apply(DelimitedDataParser.scala:48)
- com.fulcrumgenomics.commons.util.Row.apply(DelimitedDataParser.scala:52)
- com.fulcrumgenomics.bam.TrimPrimers.$anonfun$loadPrimerFile$5(TrimPrimers.scala:242)
- com.fulcrumgenomics.bam.TrimPrimers.$anonfun$loadPrimerFile$5$adapted(TrimPrimers.scala:239)
- scala.collection.Iterator.foreach(Iterator.scala:941)
- scala.collection.Iterator.foreach$(Iterator.scala:941)
- com.fulcrumgenomics.commons.util.DelimitedDataParser.foreach(DelimitedDataParser.scala:100)
- com.fulcrumgenomics.bam.TrimPrimers.loadPrimerFile(TrimPrimers.scala:239)
- com.fulcrumgenomics.bam.TrimPrimers.execute(TrimPrimers.scala:122)
- com.fulcrumgenomics.cmdline.FgBioMain.makeItSo(FgBioMain.scala:141)
- com.fulcrumgenomics.cmdline.FgBioMain.makeItSoAndExit(FgBioMain.scala:117)
- com.fulcrumgenomics.cmdline.FgBioMain$.main(FgBioMain.scala:82)
- com.fulcrumgenomics.cmdline.FgBioMain.main(FgBioMain.scala)
- at com.fulcrumgenomics.commons.reflect.ReflectionUtil$$anonfun$$nestedInanonfun$buildUnitFromString$1$2.applyOrElse(ReflectionUtil.scala:413)
- at com.fulcrumgenomics.commons.reflect.ReflectionUtil$$anonfun$$nestedInanonfun$buildUnitFromString$1$2.applyOrElse(ReflectionUtil.scala:411)
- at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:38)
- at scala.util.Failure.recover(Try.scala:234)
- at com.fulcrumgenomics.commons.reflect.ReflectionUtil$.$anonfun$buildUnitFromString$1(ReflectionUtil.scala:411)
- at scala.util.Try$.apply(Try.scala:213)
- at com.fulcrumgenomics.commons.reflect.ReflectionUtil$.buildUnitFromString(ReflectionUtil.scala:370)
- at com.fulcrumgenomics.commons.reflect.ReflectionUtil$.$anonfun$buildUnitOrOptionFromString$1(ReflectionUtil.scala:364)
- at scala.util.Try$.apply(Try.scala:213)
- at com.fulcrumgenomics.commons.reflect.ReflectionUtil$.buildUnitOrOptionFromString(ReflectionUtil.scala:363)
- at com.fulcrumgenomics.commons.reflect.ReflectionUtil$.$anonfun$typedValueFromString$1(ReflectionUtil.scala:349)
- at scala.util.Try$.apply(Try.scala:213)
- at com.fulcrumgenomics.commons.reflect.ReflectionUtil$.typedValueFromString(ReflectionUtil.scala:315)
- at com.fulcrumgenomics.commons.reflect.ReflectionUtil$.$anonfun$constructFromString$1(ReflectionUtil.scala:293)
- at scala.util.Try$.apply(Try.scala:213)
- at com.fulcrumgenomics.commons.reflect.ReflectionUtil$.constructFromString(ReflectionUtil.scala:287)
- at com.fulcrumgenomics.commons.util.Row.apply(DelimitedDataParser.scala:48)
- at com.fulcrumgenomics.commons.util.Row.apply(DelimitedDataParser.scala:52)
- at com.fulcrumgenomics.bam.TrimPrimers.$anonfun$loadPrimerFile$5(TrimPrimers.scala:242)
- at com.fulcrumgenomics.bam.TrimPrimers.$anonfun$loadPrimerFile$5$adapted(TrimPrimers.scala:239)
- at scala.collection.Iterator.foreach(Iterator.scala:941)
- at scala.collection.Iterator.foreach$(Iterator.scala:941)
- at com.fulcrumgenomics.commons.util.DelimitedDataParser.foreach(DelimitedDataParser.scala:100)
- at com.fulcrumgenomics.bam.TrimPrimers.loadPrimerFile(TrimPrimers.scala:239)
- at com.fulcrumgenomics.bam.TrimPrimers.execute(TrimPrimers.scala:122)
- at com.fulcrumgenomics.cmdline.FgBioMain.makeItSo(FgBioMain.scala:141)
- at com.fulcrumgenomics.cmdline.FgBioMain.makeItSoAndExit(FgBioMain.scala:117)
- at com.fulcrumgenomics.cmdline.FgBioMain$.main(FgBioMain.scala:82)
- at com.fulcrumgenomics.cmdline.FgBioMain.main(FgBioMain.scala)
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