Error reading large SDFile

akosgmbh · June 5, 2014, 12:46am

If I try to read a large SDFile ca. 500MB large I get the following errors:

ERROR SDFReader3NodeDialog No more tokens available: 84

What does this mean? Is there a size limit when reding SDFs?

Alex

thor · June 5, 2014, 9:11am

No there is no limit, it looks like there is an error in the SDF file somewhere. If you post the complete stacktrace from the logfile we can try to locate the erronous entry.

akosgmbh · June 5, 2014, 7:58pm

This what I see in the console:

WARN    DefaultSDFReader                 No more tokens available: 100
WARN    DefaultSDFReader                 No more tokens available: 95
WARN    DefaultSDFReader                 No more tokens available: 107
WARN    DefaultSDFReader                 No more tokens available: 89
WARN    SDF Reader                       Failed to parse 898764 record(s)

knime.log:

2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 91
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 91
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 91
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 80
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 80
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 80
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)

Alex

akosgmbh · June 5, 2014, 8:25pm

WARN    DefaultSDFReader                 No more tokens available: 104
WARN    DefaultSDFReader                 No more tokens available: 100
WARN    DefaultSDFReader                 No more tokens available: 95
WARN    DefaultSDFReader                 No more tokens available: 107
WARN    DefaultSDFReader                 No more tokens available: 89
WARN    SDF Reader                       Failed to parse 898764 record(s)

I also enclose püart of the log file:

2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 91
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 91
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 91
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 80
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 80
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 80
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 87
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 87
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 87
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 88
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 88
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 88
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 91
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 91
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 91
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 99
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 99
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 99
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 86
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 86
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 86
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 86
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 86
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 86
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 97
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 97
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 97
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 102
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 102
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 102
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 107
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 107
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 107
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 97
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 97
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 97
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 89
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 89
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 89
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 90
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 90
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 90
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 84
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 84
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 84
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 81
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 81
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 81
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(Thre

Alex

akosgmbh · June 5, 2014, 8:26pm

I enclose part of knime.log:

2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 91
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 91
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 91
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 80
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 80
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 80
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 87
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 87
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 87
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 88
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 88
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 88
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 91
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 91
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 91
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 99
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 99
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 99
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 86
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 86
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 86
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 86
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 86
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 86
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 97
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 97
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 97
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 102
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 102
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 102
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 107
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 107
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 107
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 97
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 97
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 97
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 89
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 89
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 89
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 90
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 90
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 90
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 84
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 84
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 84
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 81
2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 81
java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 81
   at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82)
   at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106)
   at org.knime.chem.base.util.sdf.SDFBlock.<init>(SDFBlock.java:80)
   at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89)
   at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373)
   at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113)
   at org.knime.core.node.NodeModel.execute(NodeModel.java:713)
   at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556)
   at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069)
   at org.knime.core.node.Node.execute(Node.java:924)
   at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418)
   at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
   at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182)
   at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
   at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
   at org.knime.core.util.ThreadPool$Worker.run(Thre

akosgmbh · June 5, 2014, 8:28pm

I add par to knime.log:

2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 91 2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 91 java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 91 at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82) at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106) at org.knime.chem.base.util.sdf.SDFBlock.(SDFBlock.java:80) at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89) at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373) at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113) at org.knime.core.node.NodeModel.execute(NodeModel.java:713) at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556) at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069) at org.knime.core.node.Node.execute(Node.java:924) at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418) at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98) at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182) at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123) at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238) 2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 80 2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 80 java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 80 at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82) at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106) at org.knime.chem.base.util.sdf.SDFBlock.(SDFBlock.java:80) at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89) at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373) at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113) at org.knime.core.node.NodeModel.execute(NodeModel.java:713) at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556) at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069) at org.knime.core.node.Node.execute(Node.java:924) at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418) at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98) at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182) at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123) at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238) 2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 87 2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 87 java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 87 at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82) at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106) at org.knime.chem.base.util.sdf.SDFBlock.(SDFBlock.java:80) at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89) at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373) at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113) at org.knime.core.node.NodeModel.execute(NodeModel.java:713) at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556) at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069) at org.knime.core.node.Node.execute(Node.java:924) at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418) at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98) at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182) at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123) at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238) 2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 88 2014-06-05 14:31:53,296 DEBUG KNIME-Worker-0 DefaultSDFReader : No more tokens available: 88 java.lang.ArrayIndexOutOfBoundsException: No more tokens available: 88 at org.knime.chem.base.util.sdf.StrTok.nextToken(StrTok.java:82) at org.knime.chem.base.util.sdf.DataItem.parseItem(DataItem.java:106) at org.knime.chem.base.util.sdf.SDFBlock.(SDFBlock.java:80) at org.knime.chem.base.util.sdf.SDFAnalyzer.analyzeSDF(SDFAnalyzer.java:89) at org.knime.chem.base.node.io.sdf.DefaultSDFReader.execute(DefaultSDFReader.java:373) at org.knime.chem.base.node.io.sdf.SDFReader3NodeModel.execute(SDFReader3NodeModel.java:113) at org.knime.core.node.NodeModel.execute(NodeModel.java:713) at org.knime.core.node.NodeModel.executeModel(NodeModel.java:556) at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:1069) at org.knime.core.node.Node.execute(Node.java:924) at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:418) at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98) at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:182) at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:113) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123) at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238) 2014-06-05 14:31:53,296 WARN KNIME-Worker-0 DefaultSDFReader : No more tokens available: 91

thor · June 6, 2014, 10:23am

It looks like some of the SDF records in the file are illegal in that they don't contain an empty line after the last property of a molecule (right before the $$$$). The SDF specification clearly states that each property/data item must be terminated by a blank line.

akosgmbh · June 7, 2014, 6:38pm

Thanks, Marvin accepts these files. This is why I was confused.

Alex

system · April 21, 2023, 9:42pm

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