Daa-meganizer command not running on command line

User Questions
1

I’m trying to meganize a daa file following a DIAMOND + MEGAN paper via the command line on an AWS server, but when I run the command no action is taken and no error is thrown except for in error.log. I run the command as so:

xvfb-run --auto-servernum --server-num=1 megan/MEGAN -g false -v true -x "megan/tools/daa-meganizer -i barcode01_unicycler.daa -mdb megan/megan-map-Feb2022.db --longReads"

I have checked the error.log file but I can’t seem to decipher what is the problem from the error text.

MEGAN fatal error:
java.lang.UnsupportedOperationException: Internal Error
Caught:
java.lang.UnsupportedOperationException: Internal Error
	at javafx.graphics/com.sun.glass.ui.gtk.GtkApplication.lambda$new$6(GtkApplication.java:223)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:319)
	at javafx.graphics/com.sun.glass.ui.gtk.GtkApplication.<init>(GtkApplication.java:200)
	at javafx.graphics/com.sun.glass.ui.gtk.GtkPlatformFactory.createApplication(GtkPlatformFactory.java:40)
	at javafx.graphics/com.sun.glass.ui.Application.run(Application.java:146)
	at javafx.graphics/com.sun.javafx.tk.quantum.QuantumToolkit.startup(QuantumToolkit.java:290)
	at javafx.graphics/com.sun.javafx.application.PlatformImpl.startup(PlatformImpl.java:292)
	at javafx.graphics/com.sun.javafx.application.PlatformImpl.startup(PlatformImpl.java:162)
	at javafx.swing/javafx.embed.swing.JFXPanel.initFx(JFXPanel.java:247)
	at javafx.swing/javafx.embed.swing.JFXPanel.<init>(JFXPanel.java:263)
	at megan/megan.main.Megan6.ensureInitFXInSwingProgram(Megan6.java:192)
	at megan/megan.main.Megan6.main(Megan6.java:78)
	at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
	at java.base/java.lang.reflect.Method.invoke(Method.java:578)
	at com.install4j.runtime/com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:84)
	at com.install4j.runtime/com.install4j.runtime.launcher.UnixLauncher.start(UnixLauncher.java:71)
	at install4j.megan.main.Megan6.main(Unknown Source)
Total time:  0.2s
Peak memory: 0 of 7.8G

Thanks in advance

2

This looks bad. Unfortunately, DAA-Meganizer is written using the Java Swing library, which expects a graphics console to be present. Using xvfb (virtual frame buffer) is supposed to fix this, but this doesn’t appear to work in your case, I will look into this.