Richard West

Thanks Rajesh - I forgot to look in your New_jobs folder. The reaction that gave the warning `Removed path reverse SPC(35105)=SPC(35107) from 0 dictionaries` is an intra_H_migration reaction, and it...

The MultiT_pdep_Prun_15000 job ended: ``` Pruning... Removed path reverse SPC(8815)=SPC(9089) from 0 dictionaries Removed path reverse SPC(17408)=SPC(17818) from 0 dictionaries Removed path reverse SPC(13368)=SPC(21650) from 0 dictionaries Removed path reverse...

The reactions A->B and B->A are both created as intra_H_migration reactions. B->A is in a pdep network for B and A->B is in a separate pdep network for A. First...

Ok, so according to @mrharper's last comment, my assumption at the top of my previous comment is slightly wrong. Perhaps we make the same path reaction twice in different PDepNetworks?...

Another example from @rajeshdparmar (listed as issue #188) Folder `~/Rajesh/New_jobs/MultiT_PM3_pdep_Prun_15000` Error Pruning... ERROR: java.lang.NullPointerException at jing.rxn.Reaction.getReactants(Reaction.java:1091) at jing.rxnSys.ReactionModelGenerator.reactionPrunableQ(ReactionModelGenerator.java:4223) at jing.rxnSys.ReactionModelGenerator.pruneReactionModel(ReactionModelGenerator.java:4111) at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1458) at RMG.main(RMG.java:96) Exception in thread "main" java.lang.NullPointerException at...

We seem to be stuck. Perhaps we could just wrap this in a try/catch block and carry on? @gmagoon, do you have any thoughts?

I've updated the debugging a bit. I suggest @rajeshdparmar now try it again, and let us know how it works out. We should check the logs for debugging messages, but...

The exception that caused these latest crashes is coming from a different place. It is now in: ``` java ERROR: java.lang.NullPointerException at jing.rxn.Reaction.getDirection(Reaction.java:924) at jing.rxnSys.ReactionModelGenerator.writePDepNetworks(ReactionModelGenerator.java:2794) at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1565) at RMG.main(RMG.java:96) ```...

Yes, it does carry on. It crashes a little later with a different NPE Richard On Jul 5, 2011, at 8:28 PM, gmagoon [email protected] wrote: > I'm a little confused...

What if `e.getStackTrace().toString()` raised an exception? Wouldn't the catch block terminate (before printing your lines) and then my bit would catch the exception and print my lines? That would lead...