Open ijobson opened 3 years ago
velkoborsky
commented
3 years ago Hello Izzy and thank you for reporting the issue.
Would you be able to try with an older version available on the Chemaxon site? There seems to be one:
If you would be interested in re-using larger parts of this project and update it to work with the latest (hopefully it is not that much to do), I am happy to help with that.
ijobson
commented
3 years ago Hi, thanks for getting back to me - I had been looking for that file for a while but couldn't find it anywhere! I've re-tried the server installation, but I'm still having a couple of problems with the GenerateHierarchy step, which is raising some issues:
> last generator/compile:run [debug] javaOptions: List(-Djna.nosys=true, -server, -Xmx8G, -XX:+UseConcMarkSweepGC) [info] Running scaffvis.Application GenerateHierarchy [info] Executing task: GenerateHierarchy. [info] Opening MapDB file /home/chris/IzzyMiniProject/scaffvis/hierarchy/processingHierarchy.mapdb [info] Opening MapDB file /home/chris/IzzyMiniProject/scaffvis/hierarchy/scaffoldHierarchy.mapdb [info] Assigning unique IDs to all scaffolds... [info] Done for level 0. [info] Done for level 1. [info] Done for level 2. [info] Done for level 3. [info] Done for level 4. [info] Done for level 5. [info] Done for level 6. java.lang.RuntimeException: Nonzero exit code returned from runner: 137 at scala.sys.package$.error(package.scala:27) at sbt.BuildCommon$$anonfun$toError$1.apply(Defaults.scala:2077) at sbt.BuildCommon$$anonfun$toError$1.apply(Defaults.scala:2077) at scala.Option.foreach(Option.scala:236) at sbt.BuildCommon$class.toError(Defaults.scala:2077) at sbt.Defaults$.toError(Defaults.scala:39) at sbt.Defaults$$anonfun$runTask$1$$anonfun$apply$38$$anonfun$apply$39.apply(Defaults.scala:750) at sbt.Defaults$$anonfun$runTask$1$$anonfun$apply$38$$anonfun$apply$39.apply(Defaults.scala:748) at scala.Function1$$anonfun$compose$1.apply(Function1.scala:47) at sbt.$tilde$greater$$anonfun$$u2219$1.apply(TypeFunctions.scala:40) at sbt.std.Transform$$anon$4.work(System.scala:63) at sbt.Execute$$anonfun$submit$1$$anonfun$apply$1.apply(Execute.scala:228) at sbt.Execute$$anonfun$submit$1$$anonfun$apply$1.apply(Execute.scala:228) at sbt.ErrorHandling$.wideConvert(ErrorHandling.scala:17) at sbt.Execute.work(Execute.scala:237) at sbt.Execute$$anonfun$submit$1.apply(Execute.scala:228) at sbt.Execute$$anonfun$submit$1.apply(Execute.scala:228) at sbt.ConcurrentRestrictions$$anon$4$$anonfun$1.apply(ConcurrentRestrictions.scala:159) at sbt.CompletionService$$anon$2.call(CompletionService.scala:28) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) 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) [error] (generator/compile:run) Nonzero exit code returned from runner: 137
Do you know if there is an easy way to resolve this?
I've also had some errors when running importPubChem and GenerateScaffolds - do I need to be concerned about these?:
importPubChem error (for some molecules): [error] Nov 17, 2020 3:46:45 PM chemaxon.marvin.io.formats.smiles.SmilesImport tetrahedralParitySmi2Mol [error] WARNING: The connectivity conditions are not fulfilled for the specified chiral center at atom 31 in the following SMILES/SMARTS: COC1=CC=C(C=C1)C2=C(C=C(C=C2)OC)N3CCC(CC3)COC4=CC(=CC=C4)[Si@@](CC(=O)O)C5CC5 [error] The chirality is ignored.
GenerateScaffolds error for native PubChem compounds: Finished processing Pubchem compounds. Total time: 783491 ms. Errors: 7.
Thanks, Izzy
Hi,
I have just started my PhD and am doing a project that involves generating scaffolds for use in deep learning, so have been trying to use your code. Unfortunately I've been having some issues, which I think are largely due to having different versions of JChem and the required libraries. I've also noticed several errors associated with chirality when importing the PubChem files.
When I load the server, there is the error 'Error calculating scaffolds from molecule' and also 'Execution exception[[RuntimeException: java.lang.NoClassDefFoundError: com/chemaxon/marvin/editor/model/properties/NonVisiblePropertyKey]]'
Do you have any ideas about how to solve these errors, or do you have a copy of the version of JChem Suite 16.1.4.0 and its associated libraries that you used to develop this code, that could help me overcome these problems?
I am running Ubuntu 20.04; Java JDK 8; JChem 20.19.0
All the best, Izzy