Bedfile command line argument wgEncodeBroadHmmGm12878HMM.bed doesn't contain both a name and a file

[Xiaoguang Pan]

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

[Aaron McKenna]

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

[Aaron McKenna]

I'm going to close this for now; if the issue still pops-up feel free to reopen it.