Hi Tiago and/or other Lositan experts,
I have a data set of 15,982 markers and 62 individuals across 4 populations. I downloaded the large sample version of Lositan and successfully loaded the genepop file into the program on my Mac. However when I run the program it crashes with the cyan message bar "simulation pass to determine initial neutral set". The java console printed this error:
Java Web Start 10.75.2.13
Using JRE version 1.7.0_75-b13 Java HotSpot(TM) 64-Bit Server VM
User home directory = /Users/garylongo
----------------------------------------------------
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>
----------------------------------------------------
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/garylongo /
15982
0.170016 34
Unhandled exception in thread started by <bound method SplitFDist.monitor of <Bio.PopGen.FDist.Async.SplitFDist object at 0x19a>>
Traceback (most recent call last):
File "/Users/garylongo/.lositan/Bio/PopGen/FDist/Async.py", line 128, in monitor
self.report_fun(fst)
File "/Users/garylongo/.lositan/Main.py", line 548, in report
selLoci = getSelLoci(pv)
File "/Users/garylongo/.lositan/Main.py", line 418, in getSelLoci
p = getP(pv[currPos])
IndexError: index out of range: 0
After some trial and error of reducing the data set size, I did get the program to run to completion when I reduced the data set to 5,002 markers. I see that the program should be able to handle 40,000 markers on Mac and 100,000 on PCs. I'm assuming this number is a product or function of sample size and not strictly loci number. Is this true? I have seen other posts that suggest reducing the size of the data set or to run separate analyzes but I would like to run the complete data set in a single run in order to analyze all my data and to avoid skewing Fst calculations in separate runs. Any suggestions would be greatly appreciated.
Thanks for your time!
Cheers,
Gary
I don't have experience with Lositan, but I have a simple and effective Fst (weir and Cockerham) for two populations. It is written in C++ and works directly from a VCF file.
https://github.com/jewmanchue/vcflib/wiki/Association-testing-with-GPAT