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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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Peptideshaker run issues #495

Open carolinelennartsson opened 1 year ago

carolinelennartsson commented 1 year ago

I have been having some issues processing files with peptideshaker and would appreciate some help figuring out the problem. I'm not sure what's the issue here, if I put anything incorrect in the input. Can you help me?

This is the error from the peptideshaker.log; com.esotericsoftware.kryo.KryoException: Encountered unregistered class ID: 95 Serialization trace: peptideAssumptionsMap (com.compomics.util.experiment.identification.matches.SpectrumMatch) at com.esotericsoftware.kryo.util.DefaultClassResolver.readClass(DefaultClassResolver.java:159) at com.esotericsoftware.kryo.Kryo.readClass(Kryo.java:758) at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:869) at com.esotericsoftware.kryo.serializers.MapSerializer.read(MapSerializer.java:235) at com.esotericsoftware.kryo.serializers.MapSerializer.read(MapSerializer.java:42) at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:799) at com.esotericsoftware.kryo.serializers.ReflectField.read(ReflectField.java:123) at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:129) at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:777) at com.compomics.util.db.object.ObjectsDB.loadFromDB(ObjectsDB.java:352) at com.compomics.util.db.object.ObjectsDB.retrieveObject(ObjectsDB.java:477) at com.compomics.util.experiment.identification.Identification.retrieveObject(Identification.java:243) at com.compomics.util.experiment.identification.Identification.getSpectrumMatch(Identification.java:258) at eu.isas.peptideshaker.processing.PsmProcessorRunnable.processPsm(PsmProcessorRunnable.java:191) at eu.isas.peptideshaker.processing.PsmProcessorRunnable.run(PsmProcessorRunnable.java:151) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:577) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at java.base/java.lang.Thread.run(Thread.java:1589) com.esotericsoftware.kryo.KryoException: java.lang.IllegalArgumentException: Can not set java.util.HashMap field com.compomics.util.experiment.identification.matches.SpectrumMatch.tagAssumptionsMap to java.lang.String Serialization trace:

hbarsnes commented 1 year ago

I'm afraid this is a known backend issue to which the only known solution is to increase the amount of memory provided to PeptideShaker. You can do this via the PeptideShaker Welcome Dialog > Settings & Help > Settings > Java Settings > Memory. Can you try increasing the memory and see if that solves the problem?

carolinelennartsson commented 1 year ago

I'm afraid that I've allowed almost my ram for this preprocessing, over 30gb. Anything else I can try?

hbarsnes commented 1 year ago

Another option you can try is to use only one thread/core. This will however dramatically slow down the processing. But could be worth it if it allows you to complete the processing. You can change this via the Processing option at the bottom of the New Project dialog.