Bedfile command line argument wgEncodeBroadHmmGm12878HMM.bed doesn't contain both a name and a file
panxiaoguang opened this issue · comments
when using BedAnnotator,I got an error:
15:25:40.024 [main] INFO modules.ScoreResults - adding score: BedAnnotator
Exception in thread "main" java.lang.AssertionError: assertion failed: Bedfile command line argument wgEncodeBroadHmmGm12878HMM.bed doesn't contain both a name and a file
at scala.Predef$.assert(Predef.scala:219)
at scoring.BedAnnotation.$anonfun$setup$1(BedAnnotation.scala:142)
at scoring.BedAnnotation.$anonfun$setup$1$adapted(BedAnnotation.scala:141)
at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:32)
at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:29)
at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:193)
at scoring.BedAnnotation.setup(BedAnnotation.scala:141)
at modules.ScoreResults.$anonfun$run$2(ScoreResults.scala:96)
at modules.ScoreResults.$anonfun$run$2$adapted(ScoreResults.scala:91)
at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:32)
at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:29)
at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:193)
at modules.ScoreResults.run(ScoreResults.scala:91)
at picocli.CommandLine.execute(CommandLine.java:1048)
at picocli.CommandLine.access$900(CommandLine.java:142)
at picocli.CommandLine$RunLast.handle(CommandLine.java:1255)
at picocli.CommandLine$RunLast.handle(CommandLine.java:1223)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:1131)
at picocli.CommandLine.parseWithHandlers(CommandLine.java:1414)
at picocli.CommandLine.parseWithHandler(CommandLine.java:1353)
at main.scala.Main$.main(Main.scala:57)
at main.scala.Main.main(Main.scala)
I use the example bed file,so why have this problem
Hi panxiaoguang,
Sorry for the slow response, somehow I missed the notification of an issue. I just ran through the example on the wiki using version 1.10 and everything worked. Any chance you could share you specific command you ran? It might also help to update to 1.10 just to make sure there isn't a version issue. Thanks!
-Aaron
I'm going to close this for now; if the issue still pops-up feel free to reopen it.