Hi,
I’ve been seeing the same thing with some of the Vernalis nodes, but I’m running into an issue with the Indigo nodes, e.g. feature remover or standardizer, where it doesn’t like the V3000 chiral annotations. Debug messages below, but also check this thread.
Thanks,
Natasja
0 …" (index 0) in row “Row0” is SDF and does not comply with its supposed superclass RDKit Molecule
org.knime.core.data.container.DataContainerException: Runtime class of object "
-INDIGO-07062011282D
0 …" (index 0) in row “Row0” is SDF and does not comply with its supposed superclass RDKit Molecule
at org.knime.core.data.container.DataContainer.checkAsyncWriteThrowable(DataContainer.java:468)
at org.knime.core.data.container.DataContainer.close(DataContainer.java:574)
at org.knime.core.data.container.RearrangeColumnsTable.create(RearrangeColumnsTable.java:385)
at org.knime.core.node.ExecutionContext.createColumnRearrangeTable(ExecutionContext.java:385)
at com.epam.indigo.knime.common.transformer.IndigoTransformerNodeModel.execute(IndigoTransformerNodeModel.java:58)
at org.knime.core.node.NodeModel.execute(NodeModel.java:737)
at org.knime.core.node.NodeModel.executeModel(NodeModel.java:571)
at org.knime.core.node.Node.invokeFullyNodeModelExecute(Node.java:1236)
at org.knime.core.node.Node.execute(Node.java:1016)
at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:557)
at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:95)
at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:218)
at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:124)
at org.knime.core.util.ThreadUtils$RunnableWithContextImpl.runWithContext(ThreadUtils.java:334)
at org.knime.core.util.ThreadUtils$RunnableWithContext.run(ThreadUtils.java:210)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:246)
Caused by: java.lang.IllegalArgumentException: Runtime class of object "
-INDIGO-07062011282D
0 …" (index 0) in row “Row0” is SDF and does not comply with its supposed superclass RDKit Molecule
at org.knime.core.data.container.DataContainer.validateSpecCompatiblity(DataContainer.java:437)
at org.knime.core.data.container.DataContainer.access$3(DataContainer.java:407)
at org.knime.core.data.container.DataContainer$ContainerRunnable.run(DataContainer.java:1229)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
2020-07-06 11:28:37,555 : DEBUG : KNIME-Worker-274-Standardizer 0:113 : : WorkflowManager : Standardizer : 0:113 : Standardizer 0:113 doBeforePostExecution
2020-07-06 11:28:37,555 : DEBUG : KNIME-Worker-274-Standardizer 0:113 : : NodeContainer : Standardizer : 0:113 : Standardizer 0:113 has new state: POSTEXECUTE
2020-07-06 11:28:37,555 : DEBUG : KNIME-Worker-274-Standardizer 0:113 : : WorkflowManager : Standardizer : 0:113 : Standardizer 0:113 doAfterExecute - failure
2020-07-06 11:28:37,555 : DEBUG : KNIME-Worker-274-Standardizer 0:113 : : Node : Standardizer : 0:113 : reset
2020-07-06 11:28:37,555 : DEBUG : KNIME-Worker-274-Standardizer 0:113 : : Node : Standardizer : 0:113 : clean output ports.
2020-07-06 11:28:37,555 : DEBUG : KNIME-Worker-274-Standardizer 0:113 : : WorkflowDataRepository : Standardizer : 0:113 : Removing handler cf4d9956-21e4-484a-ab37-e2154066073b (Standardizer 0:113: ) - 153 remaining
2020-07-06 11:28:37,555 : DEBUG : KNIME-Worker-274-Standardizer 0:113 : : NodeContainer : Standardizer : 0:113 : Standardizer 0:113 has new state: IDLE
2020-07-06 11:28:37,556 : DEBUG : KNIME-Worker-274-Standardizer 0:113 : : Node : Standardizer : 0:113 : Configure succeeded. (Standardizer)
2020-07-06 11:28:37,556 : DEBUG : KNIME-Worker-274-Standardizer 0:113 : : NodeContainer : Standardizer : 0:113 : Standardizer 0:113 has new state: CONFIGURED