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compomics / searchgui

Highly adaptable common interface for proteomics search and de novo engines
http://compomics.github.io/projects/searchgui.html
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IdentificationParametersCLI errors in latest release (1.26.5) #46

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Latest release of SearchGUI (1.26.5) fails on commandline when creating 
parameter file. Works okay with previous version.

Error recieved: 
An error occurred while loading the modifications.

Command:
java SearchGUI-1.26.5.jar eu.isas.searchgui.cmd.IdentificationParametersCLI -db 
fasta/Fly_BDGP5_24_Wolbachia_short_concatenated_target_decoy.fasta -out 
params/DDIP_embryo_fractions -fixed_mods "carboxymethyl c" -variable_mods 
"oxidation of m, phosphorylation of s, phosphorylation of t, phosphorylation of 
y, acetylation of protein n-term" 

Stripping out all mods and leaving -db and -out results in same error.

Original issue reported on code.google.com by craig.la...@gmail.com on 30 Mar 2015 at 9:44

GoogleCodeExporter commented 9 years ago 
Thanks for telling us about this. However, it all works fine on my side. Do you 
get any additional details about the error? This would make it easier for us to 
locate the problem.

Original comment by harald.b...@gmail.com on 30 Mar 2015 at 11:22

GoogleCodeExporter commented 9 years ago 
I'm able to use it with no errors on my desktop (Ubuntu 14.04), but will not 
work on the HPC cluster. Here is the rest of the output that I get:An error 
occurred while loading the modifications.
java.awt.HeadlessException: 
No X11 DISPLAY variable was set, but this program performed an operation which 
requires it.
    at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173)
    at java.awt.Window.<init>(Window.java:477)
    at java.awt.Frame.<init>(Frame.java:419)
    at java.awt.Frame.<init>(Frame.java:384)
    at javax.swing.JFrame.<init>(JFrame.java:174)
    at eu.isas.searchgui.gui.SearchGUI.<init>(SearchGUI.java:222)
    at eu.isas.searchgui.gui.SearchGUI.getJarFilePath(SearchGUI.java:4877)
    at eu.isas.searchgui.SearchHandler.getModificationsFile(SearchHandler.java:529)
    at eu.isas.searchgui.cmd.IdentificationParametersCLI.getModificationsFile(IdentificationParametersCLI.java:44)
    at com.compomics.util.experiment.identification.search_parameters_cli.AbstractIdentificationParametersCli.initiate(AbstractIdentificationParametersCli.java:48)
    at eu.isas.searchgui.cmd.IdentificationParametersCLI.<init>(IdentificationParametersCLI.java:25)
    at eu.isas.searchgui.cmd.IdentificationParametersCLI.main(IdentificationParametersCLI.java:36)
An error occurred while loading the user modifications.
java.awt.HeadlessException: 
No X11 DISPLAY variable was set, but this program performed an operation which 
requires it.
    at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173)
    at java.awt.Window.<init>(Window.java:477)
    at java.awt.Frame.<init>(Frame.java:419)
    at java.awt.Frame.<init>(Frame.java:384)
    at javax.swing.JFrame.<init>(JFrame.java:174)
    at eu.isas.searchgui.gui.SearchGUI.<init>(SearchGUI.java:222)
    at eu.isas.searchgui.gui.SearchGUI.getJarFilePath(SearchGUI.java:4877)
    at eu.isas.searchgui.SearchHandler.getUserModificationsFile(SearchHandler.java:555)
    at eu.isas.searchgui.cmd.IdentificationParametersCLI.getUserModificationsFile(IdentificationParametersCLI.java:49)
    at com.compomics.util.experiment.identification.search_parameters_cli.AbstractIdentificationParametersCli.initiate(AbstractIdentificationParametersCli.java:54)
    at eu.isas.searchgui.cmd.IdentificationParametersCLI.<init>(IdentificationParametersCLI.java:25)
    at eu.isas.searchgui.cmd.IdentificationParametersCLI.main(IdentificationParametersCLI.java:36)
An error occurred while loading the enzymes.
java.awt.HeadlessException: 
No X11 DISPLAY variable was set, but this program performed an operation which 
requires it.
    at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173)
    at java.awt.Window.<init>(Window.java:477)
    at java.awt.Frame.<init>(Frame.java:419)
    at java.awt.Frame.<init>(Frame.java:384)
    at javax.swing.JFrame.<init>(JFrame.java:174)
    at eu.isas.searchgui.gui.SearchGUI.<init>(SearchGUI.java:222)
    at eu.isas.searchgui.gui.SearchGUI.getJarFilePath(SearchGUI.java:4877)
    at eu.isas.searchgui.SearchHandler.getEnzymesFile(SearchHandler.java:542)
    at eu.isas.searchgui.cmd.IdentificationParametersCLI.getEnzymeFile(IdentificationParametersCLI.java:54)
    at com.compomics.util.experiment.identification.search_parameters_cli.AbstractIdentificationParametersCli.initiate(AbstractIdentificationParametersCli.java:60)
    at eu.isas.searchgui.cmd.IdentificationParametersCLI.<init>(IdentificationParametersCLI.java:25)
    at eu.isas.searchgui.cmd.IdentificationParametersCLI.main(IdentificationParametersCLI.java:36)
java.lang.NullPointerException
    at com.compomics.util.experiment.biology.EnzymeFactory.getEnzyme(EnzymeFactory.java:68)
    at com.compomics.util.experiment.identification.search_parameters_cli.IdentificationParametersInputBean.<init>(IdentificationParametersInputBean.java:121)
    at com.compomics.util.experiment.identification.search_parameters_cli.AbstractIdentificationParametersCli.initiate(AbstractIdentificationParametersCli.java:96)
    at eu.isas.searchgui.cmd.IdentificationParametersCLI.<init>(IdentificationParametersCLI.java:25)
    at eu.isas.searchgui.cmd.IdentificationParametersCLI.main(IdentificationParametersCLI.java:36)

I am also getting the same errors running SearchCLI with this version as well 
on our HPC cluster.
java.awt.HeadlessException: 
No X11 DISPLAY variable was set, but this program performed an operation which 
requires it.
    at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173)
    at java.awt.Window.<init>(Window.java:477)
    at java.awt.Frame.<init>(Frame.java:419)
    at java.awt.Frame.<init>(Frame.java:384)
    at javax.swing.JFrame.<init>(JFrame.java:174)
    at eu.isas.searchgui.gui.SearchGUI.<init>(SearchGUI.java:222)
    at eu.isas.searchgui.gui.SearchGUI.getJarFilePath(SearchGUI.java:4877)
    at eu.isas.searchgui.SearchHandler.getModificationsFile(SearchHandler.java:529)
    at eu.isas.searchgui.cmd.SearchCLI.<init>(SearchCLI.java:61)
    at eu.isas.searchgui.cmd.SearchCLI.main(SearchCLI.java:367)
java.awt.HeadlessException: 
No X11 DISPLAY variable was set, but this program performed an operation which 
requires it.
    at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173)
    at java.awt.Window.<init>(Window.java:477)
    at java.awt.Frame.<init>(Frame.java:419)
    at java.awt.Frame.<init>(Frame.java:384)
    at javax.swing.JFrame.<init>(JFrame.java:174)
    at eu.isas.searchgui.gui.SearchGUI.<init>(SearchGUI.java:222)
    at eu.isas.searchgui.gui.SearchGUI.getJarFilePath(SearchGUI.java:4877)
    at eu.isas.searchgui.SearchHandler.getUserModificationsFile(SearchHandler.java:555)
    at eu.isas.searchgui.cmd.SearchCLI.<init>(SearchCLI.java:67)
    at eu.isas.searchgui.cmd.SearchCLI.main(SearchCLI.java:367)
java.awt.HeadlessException: 
No X11 DISPLAY variable was set, but this program performed an operation which 
requires it.
    at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173)
    at java.awt.Window.<init>(Window.java:477)
    at java.awt.Frame.<init>(Frame.java:419)
    at java.awt.Frame.<init>(Frame.java:384)
    at javax.swing.JFrame.<init>(JFrame.java:174)
    at eu.isas.searchgui.gui.SearchGUI.<init>(SearchGUI.java:222)
    at eu.isas.searchgui.gui.SearchGUI.getJarFilePath(SearchGUI.java:4877)
    at eu.isas.searchgui.SearchHandler.getEnzymesFile(SearchHandler.java:542)
    at eu.isas.searchgui.cmd.SearchCLI.<init>(SearchCLI.java:73)
    at eu.isas.searchgui.cmd.SearchCLI.main(SearchCLI.java:367)
java.lang.UnsupportedOperationException: Path searchgui_temp not implemented.
    at eu.isas.searchgui.preferences.SearchGUIPathPreferences.setPathPreference(SearchGUIPathPreferences.java:170)
    at eu.isas.searchgui.preferences.SearchGUIPathPreferences.setAllPathsIn(SearchGUIPathPreferences.java:229)
    at eu.isas.searchgui.cmd.PathSettingsCLI.setPathSettings(PathSettingsCLI.java:48)
    at eu.isas.searchgui.cmd.SearchCLI.call(SearchCLI.java:111)
    at eu.isas.searchgui.cmd.SearchCLI.<init>(SearchCLI.java:96)
    at eu.isas.searchgui.cmd.SearchCLI.main(SearchCLI.java:367)
java.awt.HeadlessException: 
No X11 DISPLAY variable was set, but this program performed an operation which 
requires it.
    at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173)
    at java.awt.Window.<init>(Window.java:477)
    at java.awt.Frame.<init>(Frame.java:419)
    at java.awt.Frame.<init>(Frame.java:384)
    at javax.swing.JFrame.<init>(JFrame.java:174)
    at eu.isas.searchgui.gui.SearchGUI.<init>(SearchGUI.java:222)
    at eu.isas.searchgui.gui.SearchGUI.getJarFilePath(SearchGUI.java:4877)
    at eu.isas.searchgui.SearchHandler.loadSearchEngineLocation(SearchHandler.java:772)
    at eu.isas.searchgui.SearchHandler.<init>(SearchHandler.java:406)
    at eu.isas.searchgui.cmd.SearchCLI.call(SearchCLI.java:228)
    at eu.isas.searchgui.cmd.SearchCLI.<init>(SearchCLI.java:96)
    at eu.isas.searchgui.cmd.SearchCLI.main(SearchCLI.java:367)

The only difference I can see is that my machine is running java 1.7, whereas 
the cluster is running 1.6. Though this did not make any difference in 1.26.4.

Thanks

Craig

Original comment by craig.la...@gmail.com on 30 Mar 2015 at 12:12

GoogleCodeExporter commented 9 years ago 
Ok, the problem is this part: "No X11 DISPLAY variable was set, but this 
program performed an operation which requires it." I'll revert it back to the 
code used in the previous version and release a new SearchGUI version.

Original comment by harald.b...@gmail.com on 30 Mar 2015 at 12:27

GoogleCodeExporter commented 9 years ago 
SearchGUI version 1.26.6 has now been released which should fix the problem. If 
this is not the case, please let us know and we'll reopen the issue.

Original comment by harald.b...@gmail.com on 30 Mar 2015 at 1:36

GoogleCodeExporter commented 9 years ago 
Thanks Harald.

The IdentificationParametersCLI is working fine, but SearchCLI is not and is 
throwing the error:
 java.lang.UnsupportedOperationException: Path searchgui_temp not implemented.
    at eu.isas.searchgui.preferences.SearchGUIPathPreferences.setPathPreference(SearchGUIPathPreferences.java:171)
    at eu.isas.searchgui.preferences.SearchGUIPathPreferences.setAllPathsIn(SearchGUIPathPreferences.java:231)
    at eu.isas.searchgui.cmd.PathSettingsCLI.setPathSettings(PathSettingsCLI.java:48)
    at eu.isas.searchgui.cmd.SearchCLI.call(SearchCLI.java:111)
    at eu.isas.searchgui.cmd.SearchCLI.<init>(SearchCLI.java:96)
    at eu.isas.searchgui.cmd.SearchCLI.main(SearchCLI.java:367)

Again, the same command was working under 1.26.4.

Thanks

Craig

Original comment by craig.la...@gmail.com on 30 Mar 2015 at 2:42

GoogleCodeExporter commented 9 years ago 
I get the same thing on my side. I've fixed one issue, but this did not seem to 
be enough. We'll do some more testing and hopefully get back to you with a fix 
within not too long.

Original comment by harald.b...@gmail.com on 30 Mar 2015 at 4:36

GoogleCodeExporter commented 9 years ago 
Hi,

I've tried using the latest release now (1.27.1) and get the following error 
when using the command:

/mnt/lustre/scratch/mjfidcl2/SearchGUI/SearchGUI-1.27.1/SearchGUI-1.27.1.jar 
eu.isas.searchgui.cmd.IdentificationParametersCLI -db 
fasta/Fly_BDGP5_24_Wolbachia_short_concatenated_target_decoy.fasta -out 
params/DDIP_embryo_fractions
/mnt/lustre/scratch/mjfidcl2/SearchGUI/SearchGUI-1.27.1/SearchGUI-1.27.1.jar: 
line 1: PK: command not found
/mnt/lustre/scratch/mjfidcl2/SearchGUI/SearchGUI-1.27.1/SearchGUI-1.27.1.jar: 
line 2: ���F: command not found
/mnt/lustre/scratch/mjfidcl2/SearchGUI/SearchGUI-1.27.1/SearchGUI-1.27.1.jar: 
line 3: syntax error near unexpected token `)'
/mnt/lustre/scratch/mjfidcl2/SearchGUI/SearchGUI-1.27.1/SearchGUI-1.27.1.jar: 
line 3: 
���FWΔu��META-INF/MANIFEST.MF�U�n�0��?��H��4��
�%.Z�@���C/-���)Q )G��wIY�d�@
                                                                                                                                                                    ��pg_��gQ�e?AT�:�x8�=���*+,�w���7�G'�� ���2��d�3C3bͅ&R��?�u��������g�M�vRWG�%%������S�Ӌ���#������EW}�Z�q��h�|{�S��#�hJ��Ϙf��ηg0����0��L�ăԬk��X�v�yȆD����e!��*��5V�Q�N�+�qQ�$NX�*�Qْ����)XH,

Thanks

Craig

Original comment by craig.la...@gmail.com on 20 Apr 2015 at 2:23

GoogleCodeExporter commented 9 years ago 
Please ignore the last message, it hadn't not unpacked properly.

Regards

Craig

Original comment by craig.la...@gmail.com on 20 Apr 2015 at 2:37

hbarsnes commented 9 years ago

Hi Craig. I assume the issue has been fixed? If not, please let us know and we'll reopen the issue.