Shengbing Huang
Shengbing Huang
womtool graph bug: Exception in thread "main" java.util.NoSuchElementException: key not found: ScatterVariableNode(WomIdentifier(LocalName(lane),FullyQualifiedName(lane)),PlainAnonymousExpressionNode(WomIdentifier(LocalName(lane),FullyQualifiedName(lane)),WdlWomExpression(WdlExpression(),[Scatter fqn=MAPRSEQSingleSampleMasterWF.$scatter_0, item=lane, collection=MergeInputReads]),WomMaybeEmptyArrayType(WomMaybeEmptyArrayType(WomSingleFileType)),Map(MergeInputReads -> ConnectedInputPort(MergeInputReads,WomMaybeEmptyArrayType(WomMaybeEmptyArrayType(WomSingleFileType)),GraphNodeOutputPort(MAPRSEQSingleSampleMasterWF.MergeInputReads),wom.graph.GraphNode$GraphNodeSetter$$Lambda$512/0x0000000800491040@2a9fd482))),WomMaybeEmptyArrayType(WomSingleFileType)) at scala.collection.immutable.Map$EmptyMap$.apply(Map.scala:101) at scala.collection.immutable.Map$EmptyMap$.apply(Map.scala:99) at wom.views.GraphPrint$.relevantAsUpstream$1(GraphPrint.scala:177) at wom.views.GraphPrint$.upstreamPortToRelevantNodes$1(GraphPrint.scala:187) at wom.views.GraphPrint$.$anonfun$upstreamLinks$1(GraphPrint.scala:190) at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:245) at...
/biotools/biotools/eautils/1.04.807/bin/fastq-mcf -o /dlmp/qa/runs/NEUMUT/NEUMUT_092520-mgt85-1_LIB-200925-056_IL4141-P1_HHGW7BCX3/samples/20-CZJNX-A-13-00/extended/20-CZJNX-A-13-00_S2_L001_R2_001.fastq.gz /dlmp/qa/scripts/trim-adapters/onco3.fa /dlmp/qa/runs/NEUMUT/NEUMUT_092520-mgt85-1_LIB-200925-056_IL4141-P1_HHGW7BCX3/samples/20-CZJNX-A-13-00/extended/pretrim_20-CZJNX-A-13-00_S2_L001_R2_001.fastq.gz standard output: Scale used: 2.2 Phred: 33 Floating point exception