Hi everyone,
I'm trying to use progressiveMauve to align two de novo assemblies, both in
multi-fasta format. But I got error message as below:
Exception in thread "AWT-EventQueue-0" java.lang.IllegalArgumentException:
Size exceeds Integer.MAX_VALUE
at sun.nio.ch.FileChannelImpl.map(FileChannelImpl.java:707)
at org.gel.air.util.IOUtils.copyFile(Unknown Source)
at org.gel.mauve.contigs.ContigOrderer.copyInputFiles(Unknown Source)
at
org.gel.mauve.contigs.ContigMauveAlignFrame.alignButtonActionPerformed(Unkno
wn Source)
at org.gel.mauve.gui.AlignFrame$8.actionPerformed(Unknown Source)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:3
87)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
at
javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener
.java:236)
at java.awt.Component.processMouseEvent(Component.java:6041)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3265)
at java.awt.Component.processEvent(Component.java:5806)
at java.awt.Container.processEvent(Container.java:2058)
at java.awt.Component.dispatchEventImpl(Component.java:4413)
at java.awt.Container.dispatchEventImpl(Container.java:2116)
at java.awt.Component.dispatchEvent(Component.java:4243)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4322)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3986)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3916)
at java.awt.Container.dispatchEventImpl(Container.java:2102)
at java.awt.Window.dispatchEventImpl(Window.java:2440)
at java.awt.Component.dispatchEvent(Component.java:4243)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java
:273)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:18
3)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java
:173)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:168)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:160)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:121)
shown
OS name is: Linux arch: amd64
trying path /apps1/mauve/mauve_2.3.1/progressiveMauve
Executing:
/apps1/mauve/mauve_2.3.1/linux-x64/progressiveMauve
--output=/home/mauve/mauve_s1_s2.out
--output-guide-tree=/home/mauve/mauve_s1_s2.out.guide_tree
--backbone-output=/home/mauve/mauve_s1_s2.out.backbone /home/mauve/s1.fasta
/home/mauve/s2.fasta
Storing raw sequence at /tmp/rawseq25647.000
terminate called after throwing an instance of 'std::ios_base::failure'
what(): failed mapping file: Invalid argument
Exited with error code: 134
I'm using GUI, if I use command line, I only got the last four lines as
error output. Does it mean some of the input sequence is too long? Can
anyone give me some hints on how to solve this?
Thanks a million!
Robin
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