Spatial Ancestry analysis (SPA) from UCLA

Discussions concerning Autosomal DNA.

Moderator: CeCeMoore


Posts: 7
Joined: Sun Jul 22, 2012 8:57 pm
PostPosted: Fri Nov 16, 2012 4:44 am
http://genetics.cs.ucla.edu/spa/index.html has downloadable software but I am having difficulty following the directions.
I have a Mac.
I know how to get an uncompressed 23andMe file ending in .txt
I can download the SPA software. I can download and decompress the models for World and Europe.
I figured out how to make a "terminal" appear.

However I don't know how to put my 23andMe genotype file into the same directory that has the two model directories listed above. How do I get these in the same directory, whatever that is?
Under "Analyze your origin using SPA" I am lost after step 2. Maybe someone can help a non-techie person walk through the process step by step and show visual aids.
Thanks
Kathy

Posts: 43
Joined: Fri Apr 20, 2012 10:24 pm

MtDNA:
H24
PostPosted: Sat Nov 17, 2012 4:13 am
Sorry, I don't have a Mac so I can't answer your question. But I did run the program for myself and my husband. I'm mostly colonial (and presumably English) with about 1/16th German. When I run SPA for N = 1 (both parents from one ethnic background), I'm placed in Germany, which seems reasonable enough until I compare myself with my husband, who is 1/4 German and gets placed in England.

When I run my husband for N = 2, the first and second components lie right on top of one another. When I run myself for N = 2, the two components are in Sweden and Spain!
Attachments
Ann_N1&N2.JPG

Posts: 55
Joined: Fri May 25, 2012 8:11 pm
Location: United States of America
YDNA:
R-DF99/S11987
MtDNA:
H3ap
PostPosted: Mon Aug 05, 2013 7:24 pm
When I ran it I put everything in C: (genome file & spa files) then did the following commands (after --mfile type whatever your genome file's name is)

cd C:\
spa --mfile genome_Seth_Reeder_Full_20130731102500.txt --model-input europe.model --location-output europe.loc -n 2


This utility was spot on for me and consistent with the results I got from Dr. McDonald.

If a two way mix since I am of more than one ancestry group:
- My predicted first ancestry is from Kent, England
- My predicted second ancestry is from Lorraine Region, France

All of my ancestry groups are within a 1,000 km radius of SPA points:

Point 1: Kent, England

Englishmen from - chiefly Suffolk and Hampshire then Yorkshire (agnatic line), Northumberland & Durham
Ulster-Scots from - chiefly County Tyrone and County Donegal, then County Antrim, & County Cavan

Point 2: Lorraine Region, France

Mennonites from -
Alsace
Saarland
die Pfalz
Baden-Württemberg
Canton of Bern

Dr. Doug McDonald’s "most likely" prediction was 53.2% English and 46.8% French.
R-P312 clades tested for: DF99+ P312+ DF27- DF19- U152- L21- L459- Z245- L238- Z2245- Z2247-
Ysearch: VNSGW
mtDNA: H3ap
Gedmatch ID: M033622
User avatar
Posts: 84
Joined: Mon Mar 25, 2013 2:26 pm

YDNA:
R1a1a1b2a1a1
MtDNA:
Q2a
PostPosted: Wed Aug 07, 2013 3:00 am
I am using Windows 7 and I keep getting "FATAL => can't open file 23andMe.txt".

Anyone know how to fix this?

Thanks in advance.
User avatar
Posts: 387
Joined: Wed Mar 14, 2012 4:51 pm

YDNA:
R-L21>DF13**
MtDNA:
H11a2a
PostPosted: Wed Aug 07, 2013 3:19 pm
Mehrdad wrote:I am using Windows 7 and I keep getting "FATAL => can't open file 23andMe.txt".

Anyone know how to fix this?

Thanks in advance.

Make sure you put everything in a File location you have permissions to write ie

C:\Users\YourUserName\Documents\SPAwindows

Place everthing inside this location including your SPA.exe and Tar map that have been extracted (twice each)
Change the Code below to your 23andme file name and dont use the examples 23andMe.txt

./spa --mfile 23andMe.txt --model-input world.model --location-output world.loc

use this one
spa.exe --mfile mjost.txt --model-input world.model --location-output world.loc

MJost
148326 DF13** Celtic, Goidelic 111 Marker: GD1/67 & GD3/111 Watterson USA, Cook(UK/Scot Heritage) with a GD5/111, Codere(Watterson(McWalter))IOM GD8/111 and Ross Scotland GD13/111. Cluster 13*-1130-A1: 20 off-modals from L21.
Sorted slow to fast: 531=>12, 497=15, 511=11, 19=>15, 385a=12, 441=14, 552=25, 447=24, 513=11, 557=<15, 446=14, 464d=18, 456=18, 534=16, 449=31, 576=17, 710=36 and 712=>21 68-111Panel
DF13>FGC5496.
https://drive.google.com/file/d/0By9Y3j ... sp=sharing
User avatar
Posts: 387
Joined: Wed Mar 14, 2012 4:51 pm

YDNA:
R-L21>DF13**
MtDNA:
H11a2a
PostPosted: Wed Aug 07, 2013 3:52 pm
Kathy Johnston wrote:http://genetics.cs.ucla.edu/spa/index.html has downloadable software but I am having difficulty following the directions.
I have a Mac.
I know how to get an uncompressed 23andMe file ending in .txt
I can download the SPA software. I can download and decompress the models for World and Europe.
I figured out how to make a "terminal" appear.

However I don't know how to put my 23andMe genotype file into the same directory that has the two model directories listed above. How do I get these in the same directory, whatever that is?
Under "Analyze your origin using SPA" I am lost after step 2. Maybe someone can help a non-techie person walk through the process step by step and show visual aids.
Thanks
Kathy

I am sure you figured this out along time ago but other Mac'ers might wanna know how to move there files

http://www.switchingtomac.com/tutorials ... -mac-os-x/

MJost
148326 DF13** Celtic, Goidelic 111 Marker: GD1/67 & GD3/111 Watterson USA, Cook(UK/Scot Heritage) with a GD5/111, Codere(Watterson(McWalter))IOM GD8/111 and Ross Scotland GD13/111. Cluster 13*-1130-A1: 20 off-modals from L21.
Sorted slow to fast: 531=>12, 497=15, 511=11, 19=>15, 385a=12, 441=14, 552=25, 447=24, 513=11, 557=<15, 446=14, 464d=18, 456=18, 534=16, 449=31, 576=17, 710=36 and 712=>21 68-111Panel
DF13>FGC5496.
https://drive.google.com/file/d/0By9Y3j ... sp=sharing
User avatar
Posts: 387
Joined: Wed Mar 14, 2012 4:51 pm

YDNA:
R-L21>DF13**
MtDNA:
H11a2a
PostPosted: Wed Aug 07, 2013 4:15 pm
I ran my 23andme data using world and world -2 and both appear in the western half of the Atlantic straight south of Greenland.

My Europe has me in the sea between SE England and North Eastern Tip of France but my Europe -2 has me in the Atlantic west of Ireland/south of Iceland the other part in far northwestern edge of the Ukraine near Poland (tested by the Magnus Ducatus Lituaniae Project as fit for closest to Romania which would be on my maternal H11a2 side).

I must be a fish.

MJost
148326 DF13** Celtic, Goidelic 111 Marker: GD1/67 & GD3/111 Watterson USA, Cook(UK/Scot Heritage) with a GD5/111, Codere(Watterson(McWalter))IOM GD8/111 and Ross Scotland GD13/111. Cluster 13*-1130-A1: 20 off-modals from L21.
Sorted slow to fast: 531=>12, 497=15, 511=11, 19=>15, 385a=12, 441=14, 552=25, 447=24, 513=11, 557=<15, 446=14, 464d=18, 456=18, 534=16, 449=31, 576=17, 710=36 and 712=>21 68-111Panel
DF13>FGC5496.
https://drive.google.com/file/d/0By9Y3j ... sp=sharing

Posts: 55
Joined: Fri May 25, 2012 8:11 pm
Location: United States of America
YDNA:
R-DF99/S11987
MtDNA:
H3ap
PostPosted: Wed Aug 14, 2013 7:34 pm
Found a trick to the SPA - don't run the program once. Do it multiple times then find a trend. Gonna eventually get the total up to 100 and see how the figures look.

I did 40 runs total (20 runs on August 13, 2013 and another 20 on August 14, 2013).

Western Britain + Southern Germany
12 Wales + S German
5 West Mid England + S German
1 Irish Sea nearer to SE Ireland + West Austrian bordering S German
Total = 18 out of 40. Prediction occurs 45% of the time.


Northern France + North-eastern France
10 N France + NE France
Total = 10 out of 40. Prediction occurs 25% of the time.

South East England + North-eastern France
9 SE England + NE French
Total = 9 out of 40. Prediction occurs 22.5% of the time.


South East England + Southern Germany
3 SE England + S German
Total = 3 out of 40. Prediction occurs 7.5% of the time.
R-P312 clades tested for: DF99+ P312+ DF27- DF19- U152- L21- L459- Z245- L238- Z2245- Z2247-
Ysearch: VNSGW
mtDNA: H3ap
Gedmatch ID: M033622
User avatar
Posts: 287
Joined: Mon Apr 23, 2012 6:15 pm
PostPosted: Thu Aug 22, 2013 3:24 pm
MJost wrote:I must be a fish.
LOL
Barreldriver wrote:Found a trick to the SPA - don't run the program once. Do it multiple times then find a trend. Gonna eventually get the total up to 100 and see how the figures look.
Can someone confirm this observation; is SPA shuffling parameters with every run? I may would repeat an analsis I did time ago with SPA on some samples.
DNA/Admixture Central Europe (Alps, Tyrol, Dolomites, Raetia); Y-DNA J2a-L1064, J2a-L210, R1a-M17, R1b-U106 (L48-); mtDNA J1b1b, J1c1d, U5a2b2, U5b1b1. Projects : J2-M172, J2a-PF5197, Alpine DNA, ISOGG Wiki

Posts: 55
Joined: Fri May 25, 2012 8:11 pm
Location: United States of America
YDNA:
R-DF99/S11987
MtDNA:
H3ap
PostPosted: Thu Aug 22, 2013 6:42 pm
ChrisR wrote:
Barreldriver wrote:Found a trick to the SPA - don't run the program once. Do it multiple times then find a trend. Gonna eventually get the total up to 100 and see how the figures look.
Can someone confirm this observation; is SPA shuffling parameters with every run? I may would repeat an analsis I did time ago with SPA on some samples.


The more the merrier is the ideal but people don't seem to interested (it didn't take all that long to do, barely an hour or so per 20 runs done over a 3 day period for 60 runs total - that's doing the initial runs, screen capturing the google map images, organizing and posting then taking tea and bathroom breaks. It's quite expedient.). When I played around with it, it wasn't major shifting - it was alternating between already similar groups (alternating between British Islander mixed with Bavarian, British islander mixed with Rhine folks, Northern French mixed with Rhine folks).

If SPA is similar to Dr. McDonald's "spot on the map" test then it may be that SPA is coming up with multiple possibilities for ancestry that average out roughly at some spot on a map. It would help if SPA provided the same amount of literature that Dr. McDonald did with his tests (a detailed .rtf outlining what certain results mean).

My current tally:

Results (Days 1, 2 & 3. 60 runs total)

(47 out of 60 times) 78.33333% of the time it predicts one part of my ancestry as being from the British Isles and the other part from ~Germany-France (the “heart” of Europe). (13 out of 60 times) 21.66666% of the time it predicts one part of my ancestry as being from Northern France and the other part from North-eastern France. The most frequent sub-regional prediction is a Western British Islander and Southern German mix.


Western British Islander and Southern German mix
15 Wales + Southern Germany
10 West Midlands + Southern Germany
2 Irish Sea nearer to SE Ireland + Southern German/West Austrian Border
Total = 27 out of 60. Prediction occurs 45% of the time.

South East English and Southern German mix
7 South East England + Southern Germany
Total = 7 out of 60. Prediction occurs 11.66666% of the time.

South East English and North-eastern French mix
13 South East England + North-eastern France
Total = 13 out of 60. Prediction occurs 21.66666% of the time.

Northern French and North-eastern French mix
13 Northern France + North-eastern France
Total = 13 out of 60. Prediction occurs 21.66666% of the time.
R-P312 clades tested for: DF99+ P312+ DF27- DF19- U152- L21- L459- Z245- L238- Z2245- Z2247-
Ysearch: VNSGW
mtDNA: H3ap
Gedmatch ID: M033622
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