Question: How to reduce the number of SNPs for the Lositan software
gravatar for zhaojianli198322
5.6 years ago by
United States
zhaojianli1983220 wrote:

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,




lositan snp tool • 2.3k views
ADD COMMENTlink modified 5.6 years ago by Biostar ♦♦ 20 • written 5.6 years ago by zhaojianli1983220


You are using the large marker version right?

  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
ADD REPLYlink written 5.6 years ago by tiagoantao660

Hi Tiagoantao,


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?

ADD REPLYlink written 5.6 years ago by zhaojianli1983220

Hi Tiagoantao,

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

Java Web Start
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:
Missing Permissions manifest attribute in main jar:
Mac OS X /Users/jianlizhao /
*sys-package-mgr*: can't create package cache dir, 'cachedir/packages'
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/", line 128, in monitor
  File "/Users/jianlizhao/.lositan/", line 626, in report
    selLoci = getSelLoci(pv)
  File "/Users/jianlizhao/.lositan/", line 418, in getSelLoci
    p = getP(pv[currPos])
IndexError: index out of range: 0


ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by zhaojianli1983220

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

ADD REPLYlink written 4.9 years ago by jdm0

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

ADD REPLYlink written 5.6 years ago by Sean Davis26k

Hi Sean,

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

Thank you.

ADD REPLYlink written 5.6 years ago by zhaojianli1983220

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.

ADD REPLYlink written 5.6 years ago by smilefreak420

Hi Smilefreak,

I think my number is beyond the maximum amount.

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

Thank you.

ADD REPLYlink written 5.6 years ago by zhaojianli1983220
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