Problem running mauve-aligner in ubuntu 20.04.3 LTS
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Entering edit mode
9 days ago

Im trying to run mauve on my system but somehow can't seem to make it work

I installed mauve , using sudo apt install mauve-aligner But when i run it I get following error

mauve
[warning] /usr/bin/mauve: No JAVA_CMD set for run_java, falling back to JAVA_CMD = java
Exception in thread "AWT-EventQueue-0" java.lang.NumberFormatException: For input string: "."
    at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
    at java.base/java.lang.Integer.parseInt(Integer.java:638)
    at java.base/java.lang.Integer.parseInt(Integer.java:770)
    at org.gel.mauve.gui.Mauve.hasRequiredJVM(Unknown Source)
    at org.gel.mauve.gui.Mauve.init(Unknown Source)
    at org.gel.mauve.gui.Mauve$2.run(Unknown Source)
    at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
    at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
    at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
    at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
    at java.base/java.security.AccessController.doPrivileged(Native Method)
    at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
    at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
    at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
    at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
    at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
    at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
    at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
    at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

2) I then downloaded mauve and tried to run the mauve.jar file, but again I get a following error

java -jar Mauve.jar 
Exception in thread "AWT-EventQueue-0" java.lang.NumberFormatException: For input string: "."
    at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
    at java.base/java.lang.Integer.parseInt(Integer.java:638)
    at java.base/java.lang.Integer.parseInt(Integer.java:770)
    at org.gel.mauve.gui.Mauve.hasRequiredJVM(Unknown Source)
    at org.gel.mauve.gui.Mauve.init(Unknown Source)
    at org.gel.mauve.gui.Mauve$2.run(Unknown Source)
    at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
    at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
    at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
    at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
    at java.base/java.security.AccessController.doPrivileged(Native Method)
    at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
    at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
    at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
    at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
    at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
    at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
    at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
    at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

I have checked java ,

java -version
openjdk version "11.0.11" 2021-04-20
OpenJDK Runtime Environment (build 11.0.11+9-Ubuntu-0ubuntu2.20.04)
OpenJDK 64-Bit Server VM (build 11.0.11+9-Ubuntu-0ubuntu2.20.04, mixed mode, sharing)

I cant seem to figure out whats wrong in execution of the programm, I will be thankful If someone can suggest a possible solution

Genome alignment Mauve Genomics • 116 views
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Entering edit mode

mauve install instructions recommend using the binary they provide (LINK). Can you try that? If that does not work then you may have to try building from source (LINK).

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