qpAdm thread

[vbnetkhio]

I have done. However, I used a super kit(created with 3 different raw data) and had ~40MB size while an average raw data has 15-20, stating in case if it might be about it.

check if it works now:
Attachment 106247

[Kaspias]

check if it works now:
Attachment 106247

I have tried with regular MyHeritage file this time, converted it to Ancestry.

@----------------------------------------------------------@
|        PLINK!       |     v1.07      |   10/Aug/2009     |
|----------------------------------------------------------|
|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

Web-based version check ( --noweb to skip )
Connecting to web...  failed connection

Problem connecting to web

Writing this text to log file [ data_new.log ]
Analysis started: Sat Feb 27 00:52:58 2021

Options in effect:
	--file data
	--make-bed
	--out data_new

1426149 (of 1426149) markers to be included from [ data.map ]

ERROR: 
A problem with line 1 in [ data.ped ]
Expecting 6 + 2 * 1426149 = 2852304 columns, but found 2842162

The format in .ped file is as such:

name1	name2	0	0	0	1	T T	0 0	A A	A A	A A	G G	A A	G G

So actually it is how it should be. There is a blank between the alleles.

[vbnetkhio]

I have tried with regular MyHeritage file this time, converted it to Ancestry.

@----------------------------------------------------------@
|        PLINK!       |     v1.07      |   10/Aug/2009     |
|----------------------------------------------------------|
|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

Web-based version check ( --noweb to skip )
Connecting to web...  failed connection

Problem connecting to web

Writing this text to log file [ data_new.log ]
Analysis started: Sat Feb 27 00:52:58 2021

Options in effect:
	--file data
	--make-bed
	--out data_new

1426149 (of 1426149) markers to be included from [ data.map ]

ERROR: 
A problem with line 1 in [ data.ped ]
Expecting 6 + 2 * 1426149 = 2852304 columns, but found 2842162

The format in .bed file is as such:

name1	name2	0	0	0	1	T T	0 0	A A	A A	A A	G G	A A	G G

So actually it is how it should be. There is a blank between the alleles.

that looks like a very old version of plink, maybe it doesn't support tab separated .ped

try with plink 1.9:
https://www.cog-genomics.org/plink/

[Kaspias]

that looks like a very old version of plink, maybe it doesn't support tab separated .ped

try with plink 1.9:
https://www.cog-genomics.org/plink/

Possibly irregular .ped line.  Restarting scan, assuming multichar alleles.
Rescanning .ped file... 0%
Error: Half-missing call in .ped file at variant 1389874, line 1.

[vbnetkhio]

Possibly irregular .ped line.  Restarting scan, assuming multichar alleles.
Rescanning .ped file... 0%
Error: Half-missing call in .ped file at variant 1389874, line 1.

try with this one...
https://filebin.net/c73ep7a8u1pfgtxw

the "space" version should work with the older version of plink, the other one with the newer.

[Zoro]

I have tried with regular MyHeritage file this time, converted it to Ancestry.

@----------------------------------------------------------@
|        PLINK!       |     v1.07      |   10/Aug/2009     |
|----------------------------------------------------------|
|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

Web-based version check ( --noweb to skip )
Connecting to web...  failed connection

Problem connecting to web

Writing this text to log file [ data_new.log ]
Analysis started: Sat Feb 27 00:52:58 2021

Options in effect:
	--file data
	--make-bed
	--out data_new

1426149 (of 1426149) markers to be included from [ data.map ]

ERROR: 
A problem with line 1 in [ data.ped ]
Expecting 6 + 2 * 1426149 = 2852304 columns, but found 2842162

The format in .ped file is as such:

name1	name2	0	0	0	1	T T	0 0	A A	A A	A A	G G	A A	G G

So actually it is how it should be. There is a blank between the alleles.

Plink doesn’t like Ancestry format. Just convert whatever you have to 23andme format and then convert the 23andme to Plink bed bim fam. It’s super easy. Also use Plink 1.9

Ancestry alleles are tab seperated ex A A whereas 23 have no space ex AA

[vbnetkhio]

Plink doesn’t like Ancestry format. Just convert whatever you have to 23andme format and then convert the 23andme to Plink bed bim fam. It’s super easy. Also use Plink 1.9

Ancestry alleles are tab seperated ex A A whereas 23 have no space ex AA

none of the 23andme to plink scripts worked for me without errors. with my script I converted my file, and also some ancients which I had in the 23andme format successfuly.
Kaspias' file seems to have some empty fields and some fields which aren't ACGT0 so i had to adapt the script.

[Zoro]

none of the 23andme to plink scripts worked for me without errors. with my script I converted my file, and also some ancients which I had in the 23andme format successfuly.
Kaspias' file seems to have some empty fields and some fields which aren't ACGT0 so i had to adapt the script.

What do you mean?

I've converted hundreds of 23 files to plink using:

......./plink --23file sample.txt sample --out sample_plink where ..... is the path to plink executible. Highlighted sample is what the file will be named inside fam


Then you can merge your "sample" file with your "master" file using

.......//plink --bfile master --bmerge sample.bed sample.bim sample.fam --make-bed --out master_new



As far as converting some format to 23 format just post one line of your format (FTDNA, Living or whatever) and I'll make you a Unix script to convert it in 2 minutes

[vbnetkhio]

......./plink --23file sample.txt sample --out sample_plink

is that a plink function or a separate script??

edit:
found it. i wasn't aware of this function, I was using some old 23andme to ped scripts which didn't produce proper ped files.

[Zoro]

is that a plink function or a separate script??

edit:
found it. i wasn't aware of this function, I was using some old 23andme to ped scripts which didn't produce proper ped files.

Whaaaat ?

Stay as far as you can from ped files unless you absolutely have to such as converting plink to eigenstrat. They take up a ton more space than bed files