String index out of range issue

[jcanderan]

I'm having an issue with Peptideshaker. It gets to a certain point every time on a particular file then errors out.

I've re-run SearchGUI on the same file and it continues to error out. I've seen the same error on other files but they have gone away.

If you need other information, let me know.

It gets to this point:
13:18:04 Fri Jan 29 13:18:04 UTC 2021 Inferring PI Status and Sorting Proteins. Please Wait...

Then I receive the following error message:
13:18:04 Fri Jan 29 13:18:04 UTC 2021 An error occurred while creating the PeptideShaker project. Please see the PeptideShaker log file:

Here is the subsequent entry in the PeptideShaker.log file:
Fri Jan 29 13:13:53 UTC 2021: PeptideShaker version 2.0.10.
Memory given to the Java virtual machine: 42949672960.
Total amount of memory in the Java virtual machine: 42949672960.
Free memory: 42907727872.
Java version: 11.0.8-internal.
java.lang.StringIndexOutOfBoundsException
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603)
at java.base/java.util.concurrent.ForkJoinTask.reportException(ForkJoinTask.java:678)
at java.base/java.util.concurrent.ForkJoinTask.invoke(ForkJoinTask.java:737)
at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateParallel(ForEachOps.java:159)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateParallel(ForEachOps.java:173)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:233)
at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:497)
at eu.isas.peptideshaker.protein_inference.ProteinInference.inferPiStatus(ProteinInference.java:115)
at eu.isas.peptideshaker.PeptideShaker.createProject(PeptideShaker.java:626)
at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1185)
at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:243)
at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1389)
Caused by: java.lang.StringIndexOutOfBoundsException: String index out of range: 459
at java.base/java.lang.StringLatin1.charAt(StringLatin1.java:47)
at java.base/java.lang.String.charAt(String.java:693)
at com.compomics.util.experiment.identification.utils.PeptideUtils.getNEnzymaticTermini(PeptideUtils.java:530)
at com.compomics.util.experiment.identification.utils.PeptideUtils.lambda$isEnzymatic$16(PeptideUtils.java:572)
at java.base/java.util.stream.IntPipeline$4$1.accept(IntPipeline.java:246)
at java.base/java.util.Spliterators$IntArraySpliterator.tryAdvance(Spliterators.java:1041)
at java.base/java.util.stream.IntPipeline.forEachWithCancel(IntPipeline.java:163)
at java.base/java.util.stream.AbstractPipeline.copyIntoWithCancel(AbstractPipeline.java:502)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:488)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
at java.base/java.util.stream.MatchOps$MatchOp.evaluateSequential(MatchOps.java:230)
at java.base/java.util.stream.MatchOps$MatchOp.evaluateSequential(MatchOps.java:196)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.IntPipeline.anyMatch(IntPipeline.java:513)
at com.compomics.util.experiment.identification.utils.PeptideUtils.lambda$isEnzymatic$18(PeptideUtils.java:579)
at java.base/java.util.stream.MatchOps$1MatchSink.accept(MatchOps.java:90)
at java.base/java.util.ArrayList$ArrayListSpliterator.tryAdvance(ArrayList.java:1632)
at java.base/java.util.stream.ReferencePipeline.forEachWithCancel(ReferencePipeline.java:127)
at java.base/java.util.stream.AbstractPipeline.copyIntoWithCancel(AbstractPipeline.java:502)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:488)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
at java.base/java.util.stream.MatchOps$MatchOp.evaluateSequential(MatchOps.java:230)
at java.base/java.util.stream.MatchOps$MatchOp.evaluateSequential(MatchOps.java:196)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.anyMatch(ReferencePipeline.java:528)
at com.compomics.util.experiment.identification.utils.PeptideUtils.isEnzymatic(PeptideUtils.java:569)
at eu.isas.peptideshaker.protein_inference.ProteinInference.lambda$compareMainProtein$4(ProteinInference.java:403)
at java.base/java.util.stream.MatchOps$1MatchSink.accept(MatchOps.java:90)
at java.base/java.util.stream.LongPipeline$1$1.accept(LongPipeline.java:177)
at java.base/java.util.Spliterators$LongArraySpliterator.tryAdvance(Spliterators.java:1124)
at java.base/java.util.stream.LongPipeline.forEachWithCancel(LongPipeline.java:161)
at java.base/java.util.stream.AbstractPipeline.copyIntoWithCancel(AbstractPipeline.java:502)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:488)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
at java.base/java.util.stream.MatchOps$MatchOp.evaluateSequential(MatchOps.java:230)
at java.base/java.util.stream.MatchOps$MatchOp.evaluateSequential(MatchOps.java:196)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.anyMatch(ReferencePipeline.java:528)
at eu.isas.peptideshaker.protein_inference.ProteinInference.compareMainProtein(ProteinInference.java:402)
at eu.isas.peptideshaker.protein_inference.ProteinInference.inferPiStatus(ProteinInference.java:173)
at eu.isas.peptideshaker.protein_inference.ProteinInference.lambda$inferPiStatus$1(ProteinInference.java:116)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)
at java.base/java.util.HashMap$KeySpliterator.forEachRemaining(HashMap.java:1603)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
at java.base/java.util.stream.ForEachOps$ForEachTask.compute(ForEachOps.java:290)
at java.base/java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:746)
at java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:290)
at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1020)
at java.base/java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656)
at java.base/java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594)
at java.base/java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183)

[hbarsnes]

Thanks for telling us about this. Would it be possible for you to share the data you are trying to load in PeptideShaker so that we can try to reproduce and hopefully fix the issue?

[jcanderan]

I'll close this for now until I can replicate it more often. It still happens, but not consistently.
Thanks!