The includeOTs cmd line option for the score command throws the following exeption:
$ java -Xmx4g -jar FlashFry-assembly-1.9.0.jar score --includeOTs --input test_cas9ngg_targets.tsv --output test_cas9ngg_targets_scored_icludeots.tsv --scoringMetrics doench2016cfd --database test_cas9ngg_db
11:26:58.709 [main] INFO reference.binary.BinaryHeader$ - Loading header: enzyme type is SpCAS9
11:26:58.712 [main] DEBUG reference.binary.BinaryHeader$ - Number of characters used to generate this lookup file: 7
11:26:58.966 [main] INFO modules.ScoreResults - Loading CRISPR objects (filtering out overflow guides)..
11:26:59.061 [main] INFO modules.ScoreResults - adding score: Doench2014OnTarget
11:26:59.074 [main] INFO modules.ScoreResults - Scoring all guides...
11:26:59.075 [main] INFO modules.ScoreResults - Scoring with model Doench2014OnTarget
11:26:59.139 [main] INFO modules.ScoreResults - Aggregating results...
11:26:59.161 [main] INFO modules.ScoreResults - Writing annotated guides to the output file...
Exception in thread "main" picocli.CommandLine$ExecutionException: Error while running command (modules.ScoreResults@341b80b2): java.util.NoSuchElementException: key not found: 0
at picocli.CommandLine.execute(CommandLine.java:1056)
at picocli.CommandLine.access$900(CommandLine.java:142)
at picocli.CommandLine$RunAll.handle(CommandLine.java:1304)
at picocli.CommandLine$RunAll.handle(CommandLine.java:1264)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:1131)
at picocli.CommandLine.parseWithHandlers(CommandLine.java:1414)
at picocli.CommandLine.parseWithHandler(CommandLine.java:1353)
at main.scala.Main$.main(Main.scala:57)
at main.scala.Main.main(Main.scala)
Caused by: java.util.NoSuchElementException: key not found: 0
at scala.collection.MapLike.default(MapLike.scala:232)
at scala.collection.MapLike.default$(MapLike.scala:231)
at scala.collection.AbstractMap.default(Map.scala:59)
at scala.collection.mutable.HashMap.apply(HashMap.scala:65)
at bitcoding.BitPosition.decode(BitPosition.scala:67)
at crispr.CRISPRHit.$anonfun$toOutput$1(CRISPRHit.scala:43)
at crispr.CRISPRHit.$anonfun$toOutput$1$adapted(CRISPRHit.scala:42)
at scala.collection.TraversableLike.$anonfun$map$1(TraversableLike.scala:234)
at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:32)
at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:29)
at scala.collection.mutable.ArrayOps$ofLong.foreach(ArrayOps.scala:253)
at scala.collection.TraversableLike.map(TraversableLike.scala:234)
at scala.collection.TraversableLike.map$(TraversableLike.scala:227)
at scala.collection.mutable.ArrayOps$ofLong.map(ArrayOps.scala:253)
at crispr.CRISPRHit.toOutput(CRISPRHit.scala:42)
at targetio.TabDelimitedOutput.$anonfun$write$7(TabDelimitedHandler.scala:139)
at scala.collection.TraversableLike.$anonfun$map$1(TraversableLike.scala:234)
at scala.collection.mutable.ResizableArray.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ResizableArray.foreach$(ResizableArray.scala:52)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
at scala.collection.TraversableLike.map(TraversableLike.scala:234)
at scala.collection.TraversableLike.map$(TraversableLike.scala:227)
at scala.collection.AbstractTraversable.map(Traversable.scala:104)
at targetio.TabDelimitedOutput.write(TabDelimitedHandler.scala:139)
at modules.ScoreResults.$anonfun$run$8(ScoreResults.scala:131)
at modules.ScoreResults.$anonfun$run$8$adapted(ScoreResults.scala:130)
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:130)
at picocli.CommandLine.execute(CommandLine.java:1048)
... 8 more
I have tested other scoring methods and the exeption is always the same.
Details about my system:
OS: Debian GNU/Linux 9.8 (stretch)
Java version (brew install openjdk):
openjdk version "1.8.0_181-ojdkbuild"
OpenJDK Runtime Environment (build 1.8.0_181-ojdkbuild-13)
OpenJDK 64-Bit Server VM (build 25.181-b13, mixed mode)
The
includeOTs
cmd line option for thescore
command throws the following exeption:I have tested other scoring methods and the exeption is always the same. Details about my system:
brew install openjdk
):