Dear All,
I have just started having a few problems with knime 2.4.1 on Windows 7. I was investigating the use of the RDKit fingerprint node in combination with the Erl Wood Fingerprints Expander node on a set of ~ 6500 compounds.
After expanding the fingerprint I wanted to see if PCA was a good way of allowing me to visualise at least some of the chemical space spread in my set...
Anyway, prior to the PCA I thought I would get rid of the bit columns of low variance across the set using the Low Variance Filter node (setting 0.1), followed by a Normalizer on the remaining columns (54). It is at this point that I seem to be getting some strange errors - either node hanging, knime.exe runtime error, or the following error in the console window:
ERROR Normalizer Execute failed: ("GenericRDKitException"): null
WARN PCA Compute column "Bit 1" not found, selected default columns
ERROR SyncExecQueueDispatcher Uncaught exception while queuing events into main thread
I'm not quite sure why the Normalizer should be throwing an RDKit exception(?) - also, looking at the log file (see below), the whole thing seems to end with an out of memory problem (which may explain why all my node icons just turned black!).
Apologies if this isn't an RDKit issue - and if it is, I hope the log file excerpt will help track it down! : )
Kind regards
James
2011-08-02 08:05:08,798 DEBUG KNIME-Worker-0 Normalizer : reset 2011-08-02 08:05:2011-08-02 08:05:08,798 DEBUG KNIME-Worker-0 Normalizer : reset
2011-08-02 08:05:08,798 DEBUG KNIME-Worker-0 Normalizer : clean output ports.
2011-08-02 08:05:08,798 ERROR KNIME-Worker-0 Normalizer : Execute failed: ("GenericRDKitException"): null
2011-08-02 08:05:08,799 DEBUG KNIME-Worker-0 Normalizer : Execute failed: ("GenericRDKitException"): null
org.RDKit.GenericRDKitException
at org.RDKit.RDKFuncsJNI.new_Int_Vect__SWIG_1(Native Method)
at org.RDKit.Int_Vect.<init>(Int_Vect.java:43)
at org.rdkit.knime.types.RDKitMolCell2.toROMol(RDKitMolCell2.java:213)
at org.rdkit.knime.types.RDKitMolCell2.readMoleculeValue(RDKitMolCell2.java:176)
at org.rdkit.knime.types.RDKitMolValue$RDKUtilityFactory$1.compareDataValues(RDKitMolValue.java:107)
at org.knime.core.data.DataValueComparator.compare(DataValueComparator.java:123)
at org.knime.base.data.statistics.StatisticsTable.calculateAllMoments(StatisticsTable.java:273)
at org.knime.base.data.statistics.StatisticsTable.calculateAllMoments(StatisticsTable.java:218)
at org.knime.base.data.statistics.StatisticsTable.<init>(StatisticsTable.java:157)
at org.knime.base.data.normalize.Normalizer.doZScoreNorm(Normalizer.java:285)
at org.knime.base.node.preproc.normalize.NormalizerNodeModel.calculate(NormalizerNodeModel.java:318)
at org.knime.base.node.preproc.normalize.NormalizerNodeModel.execute(NormalizerNodeModel.java:281)
at org.knime.core.node.NodeModel.executeModel(NodeModel.java:524)
at org.knime.core.node.Node.execute(Node.java:873)
at org.knime.core.node.workflow.SingleNodeContainer.performExecuteNode(SingleNodeContainer.java:840)
at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:100)
at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:166)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:124)
at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:239)
2011-08-02 08:05:08,800 DEBUG KNIME-Worker-0 WorkflowManager : Normalizer 0:0:8 doBeforePostExecution
2011-08-02 08:05:08,800 DEBUG KNIME-Worker-0 NodeContainer : Normalizer 0:0:8 has new state: POSTEXECUTE
2011-08-02 08:05:08,800 DEBUG KNIME-Worker-0 KnimeResourceNavigator : Node message changed: ERROR: Error in sub flow.
2011-08-02 08:05:08,801 DEBUG KNIME-Worker-0 NodeContainer : KNIME_project3 0:0 has new state: EXECUTING
2011-08-02 08:05:08,801 DEBUG KNIME-Worker-0 WorkflowManager : Normalizer 0:0:8 doAfterExecute - failure
2011-08-02 08:05:08,801 DEBUG KNIME-Worker-0 Normalizer : reset
2011-08-02 08:05:08,801 DEBUG KNIME-Worker-0 Normalizer : clean output ports.
2011-08-02 08:05:08,801 DEBUG KNIME-Worker-0 NodeContainer : Normalizer 0:0:8 has new state: IDLE
2011-08-02 08:05:08,801 DEBUG KNIME-Worker-0 Normalizer : Configure succeeded. (Normalizer)
2011-08-02 08:05:08,801 DEBUG KNIME-Worker-0 NodeContainer : Normalizer 0:0:8 has new state: CONFIGURED
2011-08-02 08:05:08,802 WARN KNIME-Worker-0 PCA Compute : column "Bit 1" not found, selected default columns
2011-08-02 08:05:08,802 DEBUG KNIME-Worker-0 PCA Compute : Configure succeeded. (PCA Compute)
2011-08-02 08:05:08,802 DEBUG KNIME-Worker-0 NodeContainer : PCA Compute 0:0:5 has new state: CONFIGURED
2011-08-02 08:05:08,812 DEBUG KNIME-Worker-0 PCA Apply : Configure succeeded. (PCA Apply)
2011-08-02 08:05:08,812 DEBUG KNIME-Worker-0 NodeContainer : PCA Apply 0:0:6 has new state: CONFIGURED
2011-08-02 08:05:08,815 DEBUG KNIME-Worker-0 KnimeResourceNavigator : state changed to CONFIGURED
2011-08-02 08:05:08,815 DEBUG KNIME-Worker-0 NodeContainer : KNIME_project3 0:0 has new state: CONFIGURED
2011-08-02 08:05:08,815 DEBUG KNIME-Worker-0 NodeContainer : KNIME_project3 0:0 has new state: CONFIGURED
2011-08-02 08:05:08,815 DEBUG KNIME-WFM-Parent-Notifier NodeContainer : Workflow Manager 0 has new state: IDLE
2011-08-02 08:05:08,818 ERROR KNIME Sync Exec Dispatcher-1 SyncExecQueueDispatcher : Uncaught exception while queuing events into main thread
2011-08-02 08:05:08,819 DEBUG KNIME Sync Exec Dispatcher-1 SyncExecQueueDispatcher : Uncaught exception while queuing events into main thread
java.lang.OutOfMemoryError: unable to create new native thread
at java.lang.Thread.start0(Native Method)
at java.lang.Thread.start(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.tryTerminate(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.workerDone(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)