From: Jing Lu <aj...@gm...> - 2016-02-16 18:44:38
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Hi, ScaffoldHunter developers For molecule cloud function, I got the following error: 150828 [SwingWorker-pool-441706900-thread-4] INFO net.sf.jnati.deploy.artefact. ConfigManager - Loading global configuration 150828 [SwingWorker-pool-441706900-thread-4] DEBUG net.sf.jnati.deploy.artefact. ConfigManager - Loading defaults: jar:file:/C:/Users/ajing/Documents/CompareMet hods/scaffold-hunter-2.6.0/lib/cdk/cdk-1.5.13-SNAPSHOT-custom.jar!/META-INF/jnat i/jnati.default-properties 150828 [SwingWorker-pool-441706900-thread-4] INFO net.sf.jnati.deploy.artefact. ConfigManager - Loading artefact configuration: jniinchi-1.03_1 150828 [SwingWorker-pool-441706900-thread-4] DEBUG net.sf.jnati.deploy.artefact. ConfigManager - Loading instance defaults: jar:file:/C:/Users//Documents/C ompareMethods/scaffold-hunter-2.6.0/lib/cdk/cdk-1.5.13-SNAPSHOT-custom.jar!/META -INF/jnati/jnati.instance.default-properties 150828 [SwingWorker-pool-441706900-thread-4] INFO net.sf.jnati.deploy.repositor y.ClasspathRepository - Searching classpath for: jniinchi-1.03_1-WINDOWS-AMD64 150828 [SwingWorker-pool-441706900-thread-4] INFO net.sf.jnati.deploy.repositor y.LocalRepository - Searching local repository for: jniinchi-1.03_1-WINDOWS-AMD 64 150828 [SwingWorker-pool-441706900-thread-4] DEBUG net.sf.jnati.deploy.repositor y.LocalRepository - Artefact path: C:\Users\\.jnati\repo\jniinchi\1.03_1\W INDOWS-AMD64 150828 [SwingWorker-pool-441706900-thread-4] INFO net.sf.jnati.deploy.repositor y.LocalRepository - Creating artefact: C:\Users\\.jnati\repo\jniinchi\1.03 _1\WINDOWS-AMD64 150843 [SwingWorker-pool-441706900-thread-4] DEBUG net.sf.jnati.deploy.source.Ja rSource - Opening jar: C:\Users\\Documents\CompareMethods\scaffold-hunter- 2.6.0\lib\cdk\cdk-1.5.13-SNAPSHOT-custom.jar 150843 [SwingWorker-pool-441706900-thread-4] INFO net.sf.jnati.deploy.artefact. ManifestReader - Reading manifest 150890 [SwingWorker-pool-441706900-thread-4] INFO net.sf.jnati.deploy.resolver. ArtefactResolver - Copying files to repository: C:\Users\\.jnati\repo\jnii nchi\1.03_1\WINDOWS-AMD64 151109 [SwingWorker-pool-441706900-thread-4] INFO net.sf.jnati.deploy.NativeArt efactLocator - Artefact (jniinchi-1.03_1-WINDOWS-AMD64) location: C:\Users\ajin g\.jnati\repo\jniinchi\1.03_1\WINDOWS-AMD64 151109 [SwingWorker-pool-441706900-thread-4] DEBUG net.sf.jnati.deploy.NativeLib raryLoader - Loading library: C:\Users\\.jnati\repo\jniinchi\1.03_1\WINDOW S-AMD64\JniInchi-1.03_1-WINDOWS-AMD64.dll Feb 15, 2016 11:09:52 AM edu.udo.scaffoldhunter.model.util.CanonicalSmilesGenera tor createSMILES SEVERE: Smiles generation failed org.openscience.cdk.exception.CDKException: An InChI could not be generated and used to canonise SMILES: null at org.openscience.cdk.smiles.SmilesGenerator.inchiNumbers(SmilesGenerat or.java:503) at org.openscience.cdk.smiles.SmilesGenerator.labels(SmilesGenerator.jav a:471) at org.openscience.cdk.smiles.SmilesGenerator.create(SmilesGenerator.jav a:375) at org.openscience.cdk.smiles.SmilesGenerator.create(SmilesGenerator.jav a:325) at edu.udo.scaffoldhunter.model.util.CanonicalSmilesGenerator.createSMIL ES(CanonicalSmilesGenerator.java:73) at edu.udo.scaffoldhunter.model.dataimport.MergeIterator.getNextMolecule (MergeIterator.java:517) at edu.udo.scaffoldhunter.model.dataimport.MergeIterator.next(MergeItera tor.java:306) On Mon, Feb 15, 2016 at 12:27 PM, Till Schäfer < til...@tu...> wrote: > Hi, > glad to hear, that it works with the new version. > > THX for sharing the info, > Till > > Am Montag, 15. Februar 2016, 11:27:25 schrieb Jing Lu: > > Yes, you are right. The new version has no problem. > > > > > > > > Thanks, > > Jing > > > > On Mon, Feb 15, 2016 at 8:25 AM, Till Schäfer < > til...@tu... > > > wrote: > > > > > Hi, > > > the observed issue is not caused by the dataset size, but is a bug in > the > > > cdk library. Which version of SH are you using? The new SH version > 2.6.0 > > > has a new version of the cdk library. So if you are still using 2.5.1 > or > > > below, please try the new version. > > > > > > Regards, > > > Till Schäfer > > > > > > Am Freitag, 12. Februar 2016, 12:17:55 CET schrieb Jing Lu: > > > > Hi Scaffold Hunters, > > > > > > > > I have a dataset with >20,000 molecules. The software froze after > loading > > > > about 6,000 molecules and gave me the following error (part of the > > > error). > > > > > > > > Is there any way to get around this? > > > > > > > > Thanks, > > > > Jing > > > > > > > > ble.actionPerformed(SwingWorker.java:958) > > > > at javax.swing.Timer.fireActionPerformed(Unknown Source) > > > > at javax.swing.Timer$DoPostEvent.run(Unknown Source) > > > > at java.awt.event.InvocationEvent.dispatch(Unknown Source) > > > > at java.awt.EventQueue.dispatchEventImpl(Unknown Source) > > > > at java.awt.EventQueue.access$500(Unknown Source) > > > > at java.awt.EventQueue$3.run(Unknown Source) > > > > at java.awt.EventQueue$3.run(Unknown Source) > > > > at java.security.AccessController.doPrivileged(Native Method) > > > > at > > > > java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionP > > > > rivilege(Unknown Source) > > > > at java.awt.EventQueue.dispatchEvent(Unknown Source) > > > > at > java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown > > > > Source) > > > > at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown > > > Source) > > > > at > java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown > > > > Source) > > > > at java.awt.EventDispatchThread.pumpEvents(Unknown Source) > > > > at java.awt.EventDispatchThread.pumpEvents(Unknown Source) > > > > at java.awt.EventDispatchThread.run(Unknown Source) > > > > Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded > > > > at java.lang.AbstractStringBuilder.<init>(Unknown Source) > > > > at java.lang.StringBuffer.<init>(Unknown Source) > > > > at > > > org.openscience.cdk.silent.AtomType.toString(AtomType.java:366) > > > > at org.openscience.cdk.silent.Atom.toString(Atom.java:386) > > > > at java.lang.String.valueOf(Unknown Source) > > > > at java.lang.StringBuilder.append(Unknown Source) > > > > at > > > > org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis$AuxiliaryG > > > > raph.auxVertex1(SimpleCycleBasis.java:854) > > > > at > > > > org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis$AuxiliaryG > > > > raph.edgesOf(SimpleCycleBasis.java:831) > > > > at > > > > org._3pq.jgrapht.traverse.CrossComponentIterator$UndirectedSpecifics. > > > > edgesOf(Unknown Source) > > > > at > > > > org._3pq.jgrapht.traverse.CrossComponentIterator.addUnseenChildrenOf( > > > > Unknown Source) > > > > at > org._3pq.jgrapht.traverse.CrossComponentIterator.next(Unknown > > > > Source) > > > > > > > > at > > > > org.openscience.cdk.graph.MinimalPathIterator.createShortestPathGraph > > > > (MinimalPathIterator.java:143) > > > > at > > > > org.openscience.cdk.graph.MinimalPathIterator.<init>(MinimalPathItera > > > > tor.java:78) > > > > at > > > > org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis.relevantCy > > > > cles(SimpleCycleBasis.java:557) > > > > at > > > > org.openscience.cdk.ringsearch.cyclebasis.CycleBasis.relevantCycles(C > > > > ycleBasis.java:239) > > > > at > > > > org.openscience.cdk.ringsearch.SSSRFinder.findRelevantRings(SSSRFinde > > > > r.java:122) > > > > at > > > > edu.udo.scaffoldhunter.model.util.SVGGen.calcSVGString(SVGGen.java:16 > > > > 0) > > > > at > > > edu.udo.scaffoldhunter.model.util.SVGGen.getSVG(SVGGen.java:107) > > > > at > > > > edu.udo.scaffoldhunter.model.dataimport.MergeIterator.newMolecule(Mer > > > > geIterator.java:360) > > > > at > > > > edu.udo.scaffoldhunter.model.db.DbManagerHibernate.mergeMoleculesInto > > > > DBbySMILES(DbManagerHibernate.java:2545) > > > > at > > > > edu.udo.scaffoldhunter.model.dataimport.Importer$MergeWorker.doInBack > > > > ground(Importer.java:426) > > > > at > > > > edu.udo.scaffoldhunter.model.dataimport.Importer$MergeWorker.doInBack > > > > ground(Importer.java:373) > > > > at > > > > edu.udo.scaffoldhunter.gui.util.SwingWorker$1.call(SwingWorker.java:3 > > > > 18) > > > > at java.util.concurrent.FutureTask.run(Unknown Source) > > > > at > > > > edu.udo.scaffoldhunter.gui.util.SwingWorker$2.run(SwingWorker.java:32 > > > > 5) > > > > at > > > > edu.udo.scaffoldhunter.gui.util.SwingWorker.run(SwingWorker.java:362) > > > > > > > > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown > > > Source) > > > > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown > > > > Source) > > > > at java.lang.Thread.run(Unknown Source) > > > > > > > -- > > > Dipl.-Inf. Till Schäfer > > > TU Dortmund University > > > Chair 11 - Algorithm Engineering > > > Otto-Hahn-Str. 14 / Room 237 > > > 44227 Dortmund, Germany > > > > > > e-mail: til...@cs... > > > phone: +49(231)755-7706 > > > fax: +49(231)755-7740 > > > web: http://ls11-www.cs.uni-dortmund.de/staff/schaefer > > > pgp: > > > > https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84DED79 > > > > -- > Dipl.-Inf. Till Schäfer > TU Dortmund University > Chair 11 - Algorithm Engineering > Otto-Hahn-Str. 14 / Room 237 > 44227 Dortmund, Germany > > e-mail: til...@cs... > phone: +49(231)755-7706 > fax: +49(231)755-7740 > web: http://ls11-www.cs.uni-dortmund.de/staff/schaefer > pgp: > https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84DED79 > |