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compomics / meta-proteome-analyzer

MetaProteomeAnalyzer (MPA) software for analyzing and visualizing MS-based metaproteomics data.
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mpa_portable NullPointerExceptions #32

Open bernt-matthias opened 3 years ago

bernt-matthias commented 3 years ago

Having problems with MPA. Input is a 600MB fasta file and 441MB mgf. Might be a memory problem, but -Xmx 70GB is already quite a lot (actual available memory was 3 * 37GB).

Any ideas what we could try here?

stderr

Picked up _JAVA_OPTIONS: -Xmx70g -Xms256m
java.lang.NullPointerException
    at org.mapdb.DataOutput2.writeUTF(DataOutput2.java:148)
    at org.mapdb.serializer.SerializerString.serialize(SerializerString.java:15)
    at org.mapdb.serializer.SerializerString.serialize(SerializerString.java:11)
    at org.mapdb.serializer.SerializerArrayTuple.valueArraySerialize(SerializerArrayTuple.java:62)
    at org.mapdb.BTreeMapJava$NodeSerializer.serialize(BTreeMapJava.java:166)
    at org.mapdb.BTreeMapJava$NodeSerializer.serialize(BTreeMapJava.java:136)
    at org.mapdb.StoreDirectAbstract.serialize(StoreDirectAbstract.kt:243)
    at org.mapdb.StoreDirect.update(StoreDirect.kt:631)
    at org.mapdb.BTreeMap.put2(BTreeMap.kt:408)
    at org.mapdb.BTreeMap.put(BTreeMap.kt:292)
    at org.mapdb.BTreeMapJava$KeySet.add(BTreeMapJava.java:529)
    at de.mpa.io.fasta.index.OffHeapIndex.addToPeptideIndex(OffHeapIndex.java:130)
    at de.mpa.io.fasta.index.OffHeapIndex.generateIndex(OffHeapIndex.java:104)
    at de.mpa.io.fasta.index.OffHeapIndex.setupDatabase(OffHeapIndex.java:76)
    at de.mpa.io.fasta.index.OffHeapIndex.<init>(OffHeapIndex.java:58)
    at de.mpa.cli.CmdLineInterface.call(CmdLineInterface.java:222)
    at de.mpa.cli.CmdLineInterface.<init>(CmdLineInterface.java:79)
    at de.mpa.cli.CmdLineInterface.main(CmdLineInterface.java:335)

stdout

X!Tandem
DB: Merged and Filtered FASTA from data 104, data 103, and others sequences: 1260552
Spectrums:2020-06-10_LK_P24_HEW4-PA(API:9e655f38e58ae482) 
Tue Jan 26 11:12:23 CET 2021 Creating FASTA index file...
Tue Jan 26 11:31:23 CET 2021 FASTA index file creation finished...
Tue Jan 26 11:31:23 CET 2021 Creating FASTA decoy file...
Tue Jan 26 11:31:26 CET 2021 FASTA decoy file creation finished...
Tue Jan 26 11:31:26 CET 2021 Creating peptide index file...

I tried with reduced fasta files (down to 10K sequences) without success.

Turning off the option Peptide indexing (of FASTA database) circumvents the problem. But I do not know what this option is doing, i.e. if it influences the results.

This resulted in:

Picked up _JAVA_OPTIONS: -Xmx70g -Xms256m
java.lang.NullPointerException
    at de.mpa.task.instances.CreateDatabaseTask.run(CreateDatabaseTask.java:67)
    at de.mpa.task.TaskManager.run(TaskManager.java:66)
    at de.mpa.task.SearchTask.init(SearchTask.java:73)
    at de.mpa.task.SearchTask.<init>(SearchTask.java:44)
    at de.mpa.client.Client.runSearches(Client.java:134)
    at de.mpa.cli.CmdLineInterface.call(CmdLineInterface.java:251)
    at de.mpa.cli.CmdLineInterface.<init>(CmdLineInterface.java:79)
    at de.mpa.cli.CmdLineInterface.main(CmdLineInterface.java:335)

With Iterative searching and Peptide indexing (of FASTA database) disabled it seems to run through.