structure233 front-end problem

[Vikram]

Discussion group members & Dr. Pritchard,

I am experiencing some problem in using the graphical front-end to the
structure (2.3.3) program. Let me briefly explain the nature of the
problem.

1. New project is created after inputting all the required
information. In my case this is:
loci: 4184, individuals: 1548, ploidy: 2, popdata: 1, USEPOPINFO:
0, K=1-30, Burnins: 10000, MCMC: 10000
Use admixture model,

2. Once I click on "Start a job" button, I get a small window called
"Structure Job Log" which says "Start a job" and an OK button at the
bottom. Hereafter the program does nothing. If I click on OK, the
log window disappears, but the program is still not doing anything. I
confirmed this by looking at the CPU log. I have a 1.8 GHz dual core
Intel processor with almost 3GB of RAM available. The results and
simulation summary windows are empty.

I have run the exact same data file with the non-front-end version of
the program which works fine (I obtained results).

Below, I have pasted output from the shell terminal when the
graphical version of structure was invoked.

#########################

bash-3.1$ ./structure
Exception in thread "AWT-EventQueue-0"
java.lang.IllegalArgumentException: setSelectedIndex: 0 out of bounds
at javax.swing.JComboBox.setSelectedIndex(Unknown Source)
at Gui.PFileGenDlg.<init>(Unknown Source)
at Controller.PFGenManager.<init>(Unknown Source)
at Controller.StructureApp.genParamFiles(Unknown Source)
at Gui.MainFrame.actionPerformed(Unknown Source)
at javax.swing.AbstractButton.fireActionPerformed(Unknown
Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown
Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown
Source)
at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
at javax.swing.AbstractButton.doClick(Unknown Source)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown
Source)
at javax.swing.plaf.basic.BasicMenuItemUI
$Handler.mouseReleased(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown
Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown
Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown
Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown
Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown
Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown
Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
Exception in thread "AWT-EventQueue-0"
java.lang.IllegalArgumentException: setSelectedIndex: 0 out of bounds
at javax.swing.JComboBox.setSelectedIndex(Unknown Source)
at Gui.PFileGenDlg.<init>(Unknown Source)
at Controller.PFGenManager.<init>(Unknown Source)
at Controller.StructureApp.genParamFiles(Unknown Source)
at Gui.MainFrame.actionPerformed(Unknown Source)
at javax.swing.AbstractButton.fireActionPerformed(Unknown
Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown
Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown
Source)
at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
at javax.swing.AbstractButton.doClick(Unknown Source)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown
Source)
at javax.swing.plaf.basic.BasicMenuItemUI
$Handler.mouseReleased(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown
Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown
Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown
Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown
Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown
Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown
Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
Exception in thread "Thread-2" java.lang.NullPointerException
at javax.swing.text.WrappedPlainView
$WrappedLine.update(Unknown Source)
at javax.swing.text.WrappedPlainView
$WrappedLine.insertUpdate(Unknown Source)
at javax.swing.text.WrappedPlainView.insertUpdate(Unknown
Source)
at javax.swing.plaf.basic.BasicTextUI
$RootView.insertUpdate(Unknown Source)
at javax.swing.plaf.basic.BasicTextUI
$UpdateHandler.insertUpdate(Unknown Source)
at javax.swing.text.AbstractDocument.fireInsertUpdate(Unknown
Source)
at
javax.swing.text.AbstractDocument.handleInsertString(Unknown Source)
at javax.swing.text.AbstractDocument.insertString(Unknown
Source)
at javax.swing.text.PlainDocument.insertString(Unknown Source)
at javax.swing.JTextArea.append(Unknown Source)
at Controller.JobManager.run(Unknown Source)

#########################################

Thank you.

Vikram Chhatre
Texas A&M University
College Station, TX 77843
crypticlineage at gmail period com

[Thirsa-K]

Hi Vikram,

Sounds to me like you have the same problem that most people have in
the latest front-end versions of Strucutre.
As far as I know it's a bug that got into the program when version 2
was introduced and obviously hasn't been found yet. Lucky for you
there is a relatively simple solution which works for most people
(don't know why, but hey....as long as it works we're not
complaining).

The simple solution is this:

Make your project and parameter file(s) the way you always do and then
close Structure.
Open Structure again and open your project via "File - open
project" (so NOT via the "recent projects" option).
Now start the job and it should work fine.

If that doesn't work, there is another solution which may work:

Open Strucutre, make a "bogus" project and parameter file and start a
single run for that parameter file.
While that is running, open a second Structure window and in that one
open the project you want to run the job for (in this case you can use
the "recent projects" option) and start the job.
Once the job is running, you can close the window with the "bogus"
project.

If that also doesn't work, then I son't know any other solutions
anymore, so......hope one of these works.

Good luck
Thirsa

[Vikram]

Hi Thirsa,

Thanks for the reply. I tried creating the project afresh in
structure and this time it worked. It was surprisingly very fast.
But in the end, I only got plotfiles, and no results files:

1548 individuals
4184 loci
ploidy 2
10000 burnins
20000 mcmc reps
10 iterations for each value of K (1 to 30)

Results folder contains nothing
The PlotData folder contains about 300 files (10 for each value of K),
but I don't know how to open them. The simulation summary window in
structure is empty and the plots don't open up.

The program went through each simulation and showed that in the log,
but in the end nothing was obtained. This has me baffled.

Thanks
Vikram

[Thirsa-K]

There has been another discussion a little while ago about this same
problem, also with version 2.3.3 (see:
http://groups.google.com/group/structure-software/browse_thread/thread/6850371801e10fbd).

I am still running version 2.3.2 myself, because the updates made in
version 2.3.3 were not necessary for the type of data I'm running
Structure on. And I never have empty results files.

So.......if the solutions suggested in the other discussion don't work
for you (when I looked up the discussion just now I didn't read the
whole thing through, so I don't know exactly what was advised anymore)
and you don't really need version 2.3.3, I would suggest trying to go
back to version 2.3.2 and see if that works.......

> > Thirsa- Tekst uit oorspronkelijk bericht niet weergeven -
>
> - Tekst uit oorspronkelijk bericht weergeven -

[Vikram]

I just tried versions 2.3.2 and 2.3.1, with similar problem. I also
tried doing only one value of K at a time, but no difference.

Surprisingly, the backend command line version works fine, although it
seems to have less functionality (generates only one result file and
no plotfiles). It also takes incredibly lot longer to finish than the
frontend version. I don't know what to make of this.

V

On May 27, 10:57 am, Thirsa-K <t.kraaijenbr...@lumc.nl> wrote:
> There has been another discussion a little while ago about this same

> problem, also with version 2.3.3 (see:http://groups.google.com/group/structure-software/browse_thread/threa...).

[Thirsa-K]

I don't have any experience with the command line version myself, but
I would expect that it must be possible to write a batch file for it
so that it will perform multiple runs one after the other in the same
way as with the "start a job" option in the front end version.


By the way: I'm not surprised that the command line version took
longer to finish than the front end version.....after all....since
your results with the front end version were still empty, it is very
well possible that it didn't actually perform any calculations.
And not performing calculations is of course a lot faster than
actually performing calculations. ;-)