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  1. [2019/07/22 19:57:51 | FgBioMain | Info] TrimPrimers failed. Elapsed time: 0.04 minutes.
  2. Exception in thread "main" com.fulcrumgenomics.commons.reflect.ReflectionException: Could not build a 'int' from a string: : null
  3. sun.reflect.GeneratedConstructorAccessor7.newInstance(Unknown Source)
  4. sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
  5. java.lang.reflect.Constructor.newInstance(Constructor.java:423)
  6. com.fulcrumgenomics.commons.reflect.ReflectionUtil$.$anonfun$buildUnitFromString$5(ReflectionUtil.scala:398)
  7. scala.util.Try$.apply(Try.scala:213)
  8. com.fulcrumgenomics.commons.reflect.ReflectionUtil$.$anonfun$buildUnitFromString$1(ReflectionUtil.scala:394)
  9. scala.util.Try$.apply(Try.scala:213)
  10. com.fulcrumgenomics.commons.reflect.ReflectionUtil$.buildUnitFromString(ReflectionUtil.scala:370)
  11. com.fulcrumgenomics.commons.reflect.ReflectionUtil$.$anonfun$buildUnitOrOptionFromString$1(ReflectionUtil.scala:364)
  12. scala.util.Try$.apply(Try.scala:213)
  13. com.fulcrumgenomics.commons.reflect.ReflectionUtil$.buildUnitOrOptionFromString(ReflectionUtil.scala:363)
  14. com.fulcrumgenomics.commons.reflect.ReflectionUtil$.$anonfun$typedValueFromString$1(ReflectionUtil.scala:349)
  15. scala.util.Try$.apply(Try.scala:213)
  16. com.fulcrumgenomics.commons.reflect.ReflectionUtil$.typedValueFromString(ReflectionUtil.scala:315)
  17. com.fulcrumgenomics.commons.reflect.ReflectionUtil$.$anonfun$constructFromString$1(ReflectionUtil.scala:293)
  18. scala.util.Try$.apply(Try.scala:213)
  19. com.fulcrumgenomics.commons.reflect.ReflectionUtil$.constructFromString(ReflectionUtil.scala:287)
  20. com.fulcrumgenomics.commons.util.Row.apply(DelimitedDataParser.scala:48)
  21. com.fulcrumgenomics.commons.util.Row.apply(DelimitedDataParser.scala:52)
  22. com.fulcrumgenomics.bam.TrimPrimers.$anonfun$loadPrimerFile$5(TrimPrimers.scala:242)
  23. com.fulcrumgenomics.bam.TrimPrimers.$anonfun$loadPrimerFile$5$adapted(TrimPrimers.scala:239)
  24. scala.collection.Iterator.foreach(Iterator.scala:941)
  25. scala.collection.Iterator.foreach$(Iterator.scala:941)
  26. com.fulcrumgenomics.commons.util.DelimitedDataParser.foreach(DelimitedDataParser.scala:100)
  27. com.fulcrumgenomics.bam.TrimPrimers.loadPrimerFile(TrimPrimers.scala:239)
  28. com.fulcrumgenomics.bam.TrimPrimers.execute(TrimPrimers.scala:122)
  29. com.fulcrumgenomics.cmdline.FgBioMain.makeItSo(FgBioMain.scala:141)
  30. com.fulcrumgenomics.cmdline.FgBioMain.makeItSoAndExit(FgBioMain.scala:117)
  31. com.fulcrumgenomics.cmdline.FgBioMain$.main(FgBioMain.scala:82)
  32. com.fulcrumgenomics.cmdline.FgBioMain.main(FgBioMain.scala)
  33. at com.fulcrumgenomics.commons.reflect.ReflectionUtil$$anonfun$$nestedInanonfun$buildUnitFromString$1$2.applyOrElse(ReflectionUtil.scala:413)
  34. at com.fulcrumgenomics.commons.reflect.ReflectionUtil$$anonfun$$nestedInanonfun$buildUnitFromString$1$2.applyOrElse(ReflectionUtil.scala:411)
  35. at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:38)
  36. at scala.util.Failure.recover(Try.scala:234)
  37. at com.fulcrumgenomics.commons.reflect.ReflectionUtil$.$anonfun$buildUnitFromString$1(ReflectionUtil.scala:411)
  38. at scala.util.Try$.apply(Try.scala:213)
  39. at com.fulcrumgenomics.commons.reflect.ReflectionUtil$.buildUnitFromString(ReflectionUtil.scala:370)
  40. at com.fulcrumgenomics.commons.reflect.ReflectionUtil$.$anonfun$buildUnitOrOptionFromString$1(ReflectionUtil.scala:364)
  41. at scala.util.Try$.apply(Try.scala:213)
  42. at com.fulcrumgenomics.commons.reflect.ReflectionUtil$.buildUnitOrOptionFromString(ReflectionUtil.scala:363)
  43. at com.fulcrumgenomics.commons.reflect.ReflectionUtil$.$anonfun$typedValueFromString$1(ReflectionUtil.scala:349)
  44. at scala.util.Try$.apply(Try.scala:213)
  45. at com.fulcrumgenomics.commons.reflect.ReflectionUtil$.typedValueFromString(ReflectionUtil.scala:315)
  46. at com.fulcrumgenomics.commons.reflect.ReflectionUtil$.$anonfun$constructFromString$1(ReflectionUtil.scala:293)
  47. at scala.util.Try$.apply(Try.scala:213)
  48. at com.fulcrumgenomics.commons.reflect.ReflectionUtil$.constructFromString(ReflectionUtil.scala:287)
  49. at com.fulcrumgenomics.commons.util.Row.apply(DelimitedDataParser.scala:48)
  50. at com.fulcrumgenomics.commons.util.Row.apply(DelimitedDataParser.scala:52)
  51. at com.fulcrumgenomics.bam.TrimPrimers.$anonfun$loadPrimerFile$5(TrimPrimers.scala:242)
  52. at com.fulcrumgenomics.bam.TrimPrimers.$anonfun$loadPrimerFile$5$adapted(TrimPrimers.scala:239)
  53. at scala.collection.Iterator.foreach(Iterator.scala:941)
  54. at scala.collection.Iterator.foreach$(Iterator.scala:941)
  55. at com.fulcrumgenomics.commons.util.DelimitedDataParser.foreach(DelimitedDataParser.scala:100)
  56. at com.fulcrumgenomics.bam.TrimPrimers.loadPrimerFile(TrimPrimers.scala:239)
  57. at com.fulcrumgenomics.bam.TrimPrimers.execute(TrimPrimers.scala:122)
  58. at com.fulcrumgenomics.cmdline.FgBioMain.makeItSo(FgBioMain.scala:141)
  59. at com.fulcrumgenomics.cmdline.FgBioMain.makeItSoAndExit(FgBioMain.scala:117)
  60. at com.fulcrumgenomics.cmdline.FgBioMain$.main(FgBioMain.scala:82)
  61. at com.fulcrumgenomics.cmdline.FgBioMain.main(FgBioMain.scala)
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