Run fails even with Demo data

[FabianRup]

Dear Glyco-Decipher team,

unfortunately, a run fails with the following error messages even when using the Demo data:

2024-03-22 14:14:01 [Peptide Identification] Running MS-GF+ to Get PSM from De-Glyco Peak Spectrum(Several Minutes Required)
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!FAILED!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
java.lang.IllegalStateException: Index does not contain mzIdentML root!
    at uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexerFactory$MzIdentMLIndexerImpl.<init>(MzIdentMLIndexerFactory.java:106)
    at uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexerFactory$MzIdentMLIndexerImpl.<init>(MzIdentMLIndexerFactory.java:66)
    at uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexerFactory.buildIndex(MzIdentMLIndexerFactory.java:63)
    at uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexerFactory.buildIndex(MzIdentMLIndexerFactory.java:51)
    at uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller.<init>(MzIdentMLUnmarshaller.java:68)
    at edu.ucsd.msjava.mzid.MzIDParser.<init>(MzIDParser.java:32)
    at edu.ucsd.msjava.ui.MzIDToTsv.convert(MzIDToTsv.java:125)
    at edu.ucsd.msjava.ui.MzIDToTsv.main(MzIDToTsv.java:84)
    at cn.ac.dicp.group1809.utilities.msgfPlus_adapter.model.MzIDToTsv.run(MzIDToTsv.java:72)
    at cn.ac.dicp.group1809.research.glyco_decipher.gui.task.GlycoPeptideIdentificationTask.msgfPlusIdentification(GlycoPeptideIdentificationTask.java:370)
    at cn.ac.dicp.group1809.research.glyco_decipher.gui.task.GlycoPeptideIdentificationTask.call(GlycoPeptideIdentificationTask.java:128)
    at cn.ac.dicp.group1809.research.glyco_decipher.gui.task.GlycoPeptideIdentificationTask.call(GlycoPeptideIdentificationTask.java:54)
    at javafx.concurrent.Task$TaskCallable.call(Task.java:1426)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.lang.Thread.run(Thread.java:834)

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!FAILED!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!FAILED!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
java.lang.IllegalStateException: Index does not contain mzIdentML root!
    at uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexerFactory$MzIdentMLIndexerImpl.<init>(MzIdentMLIndexerFactory.java:106)
    at uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexerFactory$MzIdentMLIndexerImpl.<init>(MzIdentMLIndexerFactory.java:66)
    at uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexerFactory.buildIndex(MzIdentMLIndexerFactory.java:63)
    at uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexerFactory.buildIndex(MzIdentMLIndexerFactory.java:51)
    at uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller.<init>(MzIdentMLUnmarshaller.java:68)
    at edu.ucsd.msjava.mzid.MzIDParser.<init>(MzIDParser.java:32)
    at edu.ucsd.msjava.ui.MzIDToTsv.convert(MzIDToTsv.java:125)
    at edu.ucsd.msjava.ui.MzIDToTsv.main(MzIDToTsv.java:84)
    at cn.ac.dicp.group1809.utilities.msgfPlus_adapter.model.MzIDToTsv.run(MzIDToTsv.java:72)
    at cn.ac.dicp.group1809.research.glyco_decipher.gui.task.GlycoPeptideIdentificationTask.msgfPlusIdentification(GlycoPeptideIdentificationTask.java:370)
    at cn.ac.dicp.group1809.research.glyco_decipher.gui.task.GlycoPeptideIdentificationTask.call(GlycoPeptideIdentificationTask.java:128)
    at cn.ac.dicp.group1809.research.glyco_decipher.gui.task.GlycoPeptideIdentificationTask.call(GlycoPeptideIdentificationTask.java:54)
    at javafx.concurrent.Task$TaskCallable.call(Task.java:1426)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.lang.Thread.run(Thread.java:834)

[DICP-1809]

We re-checked our software carefully with Demo data, and it worked very well in this step:

The error was reported during .mzid result file conversion. I found similar issue was reported in 2017 for jmzml package (https://github.com/PRIDE-Utilities/jmzml/issues/20), which was used in our software. But we have never met issue like this. Please:

1. check that you have downloaded the correct demo date file and closed any editing window when searching this file.
2. delete the "temp_demo" directory, and try to re-search the file.

[FabianRup]

Thank you, the DemoData now ran successfully. Using first real data, I get the following error:

2024-03-22 15:01:02 [Peptide Identification] Running MS-GF+ to Get PSM from De-Glyco Peak Spectrum(Several Minutes Required)
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!FAILED!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
    at cn.ac.dicp.group1809.utilities.uniprot_reader.fasta.FastaParser.read(FastaParser.java:58)
    at cn.ac.dicp.group1809.research.glyco_decipher.utils.MotifContainingProtein.write(MotifContainingProtein.java:32)
    at cn.ac.dicp.group1809.research.glyco_decipher.gui.task.GlycoPeptideIdentificationTask.msgfPlusPreProcess(GlycoPeptideIdentificationTask.java:317)
    at cn.ac.dicp.group1809.research.glyco_decipher.gui.task.GlycoPeptideIdentificationTask.msgfPlusIdentification(GlycoPeptideIdentificationTask.java:358)
    at cn.ac.dicp.group1809.research.glyco_decipher.gui.task.GlycoPeptideIdentificationTask.call(GlycoPeptideIdentificationTask.java:128)
    at cn.ac.dicp.group1809.research.glyco_decipher.gui.task.GlycoPeptideIdentificationTask.call(GlycoPeptideIdentificationTask.java:54)
    at javafx.concurrent.Task$TaskCallable.call(Task.java:1426)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.lang.Thread.run(Thread.java:834)

[DICP-1809]

The error was reported when reading your fasta protein database, and was caused by invalid protein header format. Now our software only recognizes UniProt Protein Header format (please reference https://www.uniprot.org/help/fasta-headers):

which contains three main parts split with "|": a|b|c in which a: database; b: protein accession; c: protein annotation. When reading your fasta, the software failed to get protein accession information of the second part. We provided a fasta file in demo, which is a protein database for mouse. You can:

1. reference this to change your own fasta protein header format (just place accession at the middle of "|" splited values of protein header);
2. or download a new standard fasta file from UniProt: https://www.uniprot.org/

[FabianRup]

Thank you so much for the quick answer, this was indeed the problem!

It would be nice in future releases if the fasta header wouldn't play such a big role. This is particularly interesting for people working on non-model species that don't have a proteome available in uniprot.