Lositan freezes when producing selection table

Question

[mhmeek]

I'm running Lositan on a dataset with 465 individuals typed at 11,783 SNP loci. I can load the data and run the simulation, but then when it says "Done (preparing selection table, please wait...)" it just freezes and never produces the table. What can I do to fix this?

Thanks!

[tiagoantao]

Could you please configure your Java virtual machine (On windows, you can find this on the control panel) to start up the console and always show it? Then run your dataset, get the error that gets out and post it here?

[mhmeek]

Yes, here is what I got:

Java Web Start 10.67.2.01
Using JRE version 1.7.0_67-b01 Java HotSpot(TM) 64-Bit Server VM
User home directory = /Users/mhmeek
----------------------------------------------------
c:   clear console window
f:   finalize objects on finalization queue
g:   garbage collect
h:   display this help message
m:   print memory usage
o:   trigger logging
p:   reload proxy configuration
q:   hide console
r:   reload policy configuration
s:   dump system and deployment properties
t:   dump thread list
v:   dump thread stack
0-5: set trace level to <n>
----------------------------------------------------

CacheEntry[http://popgen.net/soft/lositan/code2/lib/jcommon-1.0.16.jar]: updateAvailable=true,lastModified=Wed Jul 16 05:08:10 PDT 2014,length=-1
CacheEntry[http://popgen.net/soft/lositan/code2/lib/jython.jar]: updateAvailable=true,lastModified=Wed Jul 16 05:08:12 PDT 2014,length=-1
CacheEntry[http://popgen.net/soft/lositan/code2/lib/jfreechart-1.0.13.jar]: updateAvailable=true,lastModified=Wed Jul 16 05:08:10 PDT 2014,length=-1
CacheEntry[http://popgen.net/soft/lositan/code2/lib/selwb.jar]: updateAvailable=true,lastModified=Wed Jul 16 05:08:12 PDT 2014,length=-1
CacheEntry[http://popgen.net/soft/lositan/code2/lib/batik-awt-util.jar]: updateAvailable=true,lastModified=Wed Jul 16 05:08:09 PDT 2014,length=-1
CacheEntry[http://popgen.net/soft/lositan/code2/lib/batik-dom.jar]: updateAvailable=true,lastModified=Wed Jul 16 05:08:09 PDT 2014,length=-1
CacheEntry[http://popgen.net/soft/lositan/code2/lib/batik-svggen.jar]: updateAvailable=true,lastModified=Wed Jul 16 05:08:09 PDT 2014,length=-1
CacheEntry[http://popgen.net/soft/lositan/code2/lib/batik-util.jar]: updateAvailable=true,lastModified=Wed Jul 16 05:08:09 PDT 2014,length=-1
CacheEntry[http://popgen.net/soft/lositan/code2/lib/batik-xml.jar]: updateAvailable=true,lastModified=Wed Jul 16 05:08:10 PDT 2014,length=-1
CacheEntry[http://popgen.net/soft/lositan/code2/lib/iText-2.1.5.jar]: updateAvailable=true,lastModified=Wed Jul 16 05:08:10 PDT 2014,length=-1
Missing Application-Name manifest attribute for: http://popgen.net/soft/lositan/code2/lib/selwb.jar
Missing Permissions manifest attribute in main jar: http://popgen.net/soft/lositan/code2/lib/selwb.jar
Mac OS X /Users/mhmeek /
11783
0.027196 46
Unhandled exception in thread started by <bound method SplitFDist.monitor of <Bio.PopGen.FDist.Async.SplitFDist object at 0x5a>>
Traceback (most recent call last):
  File "/Users/mhmeek/.lositan/Bio/PopGen/FDist/Async.py", line 128, in monitor
    self.report_fun(fst)
  File "/Users/mhmeek/.lositan/Main.py", line 626, in report
    selLoci = getSelLoci(pv)
  File "/Users/mhmeek/.lositan/Main.py", line 418, in getSelLoci
    p = getP(pv[currPos])
IndexError: index out of range: 0

[tiagoantao]

Hi,

Can you try this on Windows to see if you have the same error (or a Windows emulator, or Linux)? I do not have a Mac and would need to see if this error replicates on any of the platforms that I have access to.

Answer 1

[gregoryneil.puncher2]

Hello, was this problem sorted? I am having the same problem in windows. Lositan just freezes at the last step and does not produce the tables.