How to reduce the number of SNPs for the Lositan software

Question

[zhaojianli198322]

Hi guys,

I'm learning Lositan to find outliers from SNP. I think because my number of SNP (115740) exceed to the capability of Lositan, it stopped at the calculating step.

I think the Biopython version may revolve this problem, but I don't know how to execute your python script. Would anyone like give some instructions? or do you have any other idea to resolve the large data set?

All the best, Jianli

[tiagoantao]

Hi,

You are using the large marker version right? http://www.popgen.net/soft/lositan/3264.html

1. What is your operating system?
2. Could you please start the Java console and post the error here?
3. If I remember well the limit is 100,000 (less on Mac, like 40,000). If you randomly trim the genepop file, you should be OK

[zhaojianli198322]

Hi Tiagoantao,

Thanks.

I used the large marker version.

1. I used the Mac system.
2. there was no error report. It just was frozen at window "Done (preparing selection table, please wait".
3. My SNP number is 114,740. I think this may be the problem. would you like tell me how to trim the genepop file randomly?

[zhaojianli198322]

Hi Tiagoantao,

I get the java console error report. Do you have more suggestion? Thank you.

Java Web Start 11.25.2.17
Using JRE version 1.8.0_25-b17 Java HotSpot(TM) 64-Bit Server VM
User home directory = /Users/jianlizhao
----------------------------------------------------
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/jianlizhao /
*sys-package-mgr*: can't create package cache dir, 'cachedir/packages'
115266
0.350918 9
Unhandled exception in thread started by <bound method SplitFDist.monitor of <Bio.PopGen.FDist.Async.SplitFDist object at 0xaa>>
Traceback (most recent call last):
  File "/Users/jianlizhao/.lositan/Bio/PopGen/FDist/Async.py", line 128, in monitor
    self.report_fun(fst)
  File "/Users/jianlizhao/.lositan/Main.py", line 626, in report
    selLoci = getSelLoci(pv)
  File "/Users/jianlizhao/.lositan/Main.py", line 418, in getSelLoci
    p = getP(pv[currPos])
IndexError: index out of range: 0

[jdm]

I get the same error, although my dataset has 8189 SNPs. Did you ever resolve the issue?

[Sean Davis]

What is the error you received? What versions of the software are you using?

[zhaojianli198322]

Hi Sean,

There was no error report. I'm using the latest Lositan.

Thank you.

[smilefreak]

Do you happen to know what the maximum amount allowed is?

If so you could use the unix split command to split into files for processing in Lositan.

[zhaojianli198322]

Hi Smilefreak,

I think my number is beyond the maximum amount.

Do you know how to split the file using unix command?

Thank you.