using deNovoGUI from cmd LINUX

Irina Tarasova

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Aug 31, 2021, 12:20:50 PM8/31/21

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Dear Colleagues,

I'm trying to run deNovoGUI from cmd line using our LINUX machine:

java -cp /home/lab006/DeNovoGUI-1.16.6/DeNovoGUI-1.16.6.jar com.compomics.denovogui.cmd.DeNovoCLI \
-spectrum_files /home/lab006/DeNovoGUI-1.16.6/resources/reference_dataset/Arabidopsis_P1_Top5CID_01.mgf \
-output_folder $output \
-id_params /home/lab006/DeNovoGUI-1.16.6/resources/reference_dataset/denovoGUI_example.par

However, error message is generated:

An error occurred while importing the parameters file /home/lab006/DeNovoGUI-1.16.6/resources/reference_dataset/denovoGUI_example.par. java.lang.NullPointerException: Cannot invoke "java.util.ArrayList.size()" because "list1" is null at com.compomics.util.Util.sameLists(Util.java:817) at com.compomics.util.experiment.identification.identification_parameters.SearchParameters.getShortDescription(SearchParameters.java:912) at com.compomics.util.preferences.IdentificationParameters.setSearchParameters(IdentificationParameters.java:157) at com.compomics.util.preferences.IdentificationParameters.setParametersFromSearch(IdentificationParameters.java:523) at com.compomics.util.preferences.IdentificationParameters.<init>(IdentificationParameters.java:101) at com.compomics.util.preferences.IdentificationParameters.getIdentificationParameters(IdentificationParameters.java:426) at com.compomics.cli.identification_parameters.IdentificationParametersInputBean.isValidStartup(IdentificationParametersInputBean.java:170) at com.compomics.denovogui.cmd.DeNovoCLIInputBean.isValidStartup(DeNovoCLIInputBean.java:327) at com.compomics.denovogui.cmd.DeNovoCLI.<init>(DeNovoCLI.java:62) at com.compomics.denovogui.cmd.DeNovoCLI.main(DeNovoCLI.java:366)

Is it my mistake or bug?

First I tried my own params generated using GUI, but they were not recognized. Then I attempt to run denovogui example set and it failed again.

Looking forward your advice,

Irina

Harald Barsnes

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Sep 1, 2021, 8:03:49 AM9/1/21

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Hi Irina,

Thanks for letting us know. I'm not able to reproduce the issue though. Can you try using the parameter file from the example dataset as well? You'll find it in the DeNovoGUI-1.16.6\example_dataset folder.

It would also be great if you could share the parameter files that do not work correctly?

Best regards,

Harald

Irina Tarasova

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Sep 1, 2021, 9:35:49 AM9/1/21

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Hi Harald,

thank you very much for quick response.

Well.. lets start..

Try #1 (with example_dataset/denovo.par ):

[ira@calc-server ~]$ java -cp /home/lab006/DeNovoGUI-1.16.6/DeNovoGUI-1.16.6.jar com.compomics.denovogui.cmd.DeNovoCLI -spectrum_files /home/lab006/DeNovoGUI-1.16.6/example_dataset/Ecoli_30.mgf -output_folder /home/ira/ -id_params /home/lab006/DeNovoGUI-1.16.6/example_dataset/denovo.par               java.lang.reflect.InaccessibleObjectException: Unable to make field int java.awt.Color.value accessible: module java.desktop does not "opens java.awt" to unnamed module @4b4523f8
        at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:357)
        at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
        at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:177)
        at java.base/java.lang.reflect.Field.setAccessible(Field.java:171)
        at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.getBoundFields(ReflectiveTypeAdapterFactory.java:154)
        at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.create(ReflectiveTypeAdapterFactory.java:97)
        at com.google.gson.Gson.getAdapter(Gson.java:360)
        at com.google.gson.internal.bind.MapTypeAdapterFactory.create(MapTypeAdapterFactory.java:126)
        at com.google.gson.Gson.getAdapter(Gson.java:360)
        at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.getFieldAdapter(ReflectiveTypeAdapterFactory.java:136)
        at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.access$100(ReflectiveTypeAdapterFactory.java:49)
        at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$1.<init>(ReflectiveTypeAdapterFactory.java:106)
        at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.createBoundField(ReflectiveTypeAdapterFactory.java:105)
        at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.getBoundFields(ReflectiveTypeAdapterFactory.java:161)
        at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.create(ReflectiveTypeAdapterFactory.java:97)
        at com.google.gson.Gson.getAdapter(Gson.java:360)
        at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.getFieldAdapter(ReflectiveTypeAdapterFactory.java:136)
        at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.access$100(ReflectiveTypeAdapterFactory.java:49)
        at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$1.<init>(ReflectiveTypeAdapterFactory.java:106)
        at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.createBoundField(ReflectiveTypeAdapterFactory.java:105)
        at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.getBoundFields(ReflectiveTypeAdapterFactory.java:161)
        at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.create(ReflectiveTypeAdapterFactory.java:97)
        at com.google.gson.Gson.getAdapter(Gson.java:360)
        at com.google.gson.Gson.fromJson(Gson.java:813)
        at com.google.gson.Gson.fromJson(Gson.java:779)
        at com.google.gson.Gson.fromJson(Gson.java:728)
        at com.google.gson.Gson.fromJson(Gson.java:700)
        at com.compomics.util.io.json.JsonMarshaller.fromJson(JsonMarshaller.java:122)
        at com.compomics.util.experiment.identification.identification_parameters.SearchParameters.getIdentificationParameters(SearchParameters.java:779)
        at com.compomics.denovogui.cmd.DeNovoCLIInputBean.isValidStartup(DeNovoCLIInputBean.java:317)