Problem running mauve-aligner in ubuntu 20.04.3 LTS

Question

[shrivadeepak]

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

[GenoMax]

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).

Answer 1

[Joshua]

I managed to fix this same error. As far as I can tell, it comes from Mauve not running wsell with Java 10+ versions.

I used

$ locate java | grep java$ | grep -w bin

to find a version of java that was sufficiently outdated to work with Mauve. I foudn a 7.0 version in a different users files.

I then manually edited the Mauve file in my Mauve install, and changed the JAVA_CMD=java to JAVA_CMD=path/to/older/version/java

I hope this helps!

[nick.carleson]

If anyone else lands here from Google: Using Java 7 resolved this error for me. I created an Oracle account and downloaded it from their archive