Problems running ADMIXTURE software

[Ingrid]

I'm trying to run an analysin with the --supervised flag.
This in the advice of the manual on how to do that:
Supervised learning mode is enabled with the
ag --supervised and requires an additional
le with a .pop su x, specifying the ancestries of the reference individuals. It is assumed
that all reference samples have 100% ancestry from some ancestral population. Each line
of the .pop le corresponds to individual listed on the same line number in the .fam or
.ped le. If the individual is a population reference, the .pop le line should be a string
(beginning with an alphanumeric character) designating the population. If the individual
is of unknown ancestry, use \-" (or a blank line, or any non-alphanumeric character) to
indicate that the ancestry should be estimated.

I prepared the .pop file and I tryed tu give the command
but seems it is not recognized by the program and I don't even receive an ERROR message.

this is the command line I gave:

admixture --supervised filename.pop filename.bed 4

as I said I'm trying different way to write it but still is not working.

Any idea?

thank you all
Ingrid

[Vikram Chhatre]

Ingrid -

Since this isn't a discussion group dedicated to ADMIXTURE software, I don't know how much luck you will have getting help here.  So you may also want to contact the software author if the following doesn't resolve your issues.

1. If you are using commandline to launch the program on Unix like operating systems, try "./admixture"  (dot slash command).

2. Is your .pop file named 'filename.pop'?  If not, you will need to change it.  For example 'Ingrid_Data.pop'.  Same thing for filename.bed.

All the best

V

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[shalanee weerasinghe]

Dear Ingrid,

When you prepare your pop file which include the reference populations and the unknown populations with blanks,

Please use following command

./admixture filname.bed 4 --supervised

Your bed file (filename.bed), map file (filename.map) and pop file(filename.pop) should be in your working directory

Hope this will help you


Shalanee
PhD candidate,
UNE

[Ingrid]

Thanks guys
at the end I managed to make it work!
I used EmEditor to prepare the pop file and the command line as suggested Shalanee.

Was not a big problem but still is nice to know that you all guys are here ready to help!!!
thanks everybody!
:*:)

[Dr. Ozlem Ozbek]

Dear all members in the group

I have protein data for 10 einkorn wheat landraces populations. I analysed the data by using structure program. Then I calculated K as 11. In the output file of k11 individual I also counted 11 colours. But one of the colour is observed in verysmall number of member. I supposed to get lower number for k than 10. But I get higher number than even I anaysed. This is so strange. So, anyone can help me about my results? Thank you.

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--

Asst.Prof. Özlem ÖZBEK, Ph.D
Hitit Üniversity
Faculty of Art and Science
Department of Biology

19030-CORUM/TURKEY
Tel    : +90 364 2277000/1612
Faks : +90 364 2277005
e-mail: ozbek...@gmail.com

[Vikram Chhatre]

Hi Ozlem -

Can you post your lnPD and deltaK graphs as well as bar plots?  Please start a new thread to avoid mixing up two different topics.

Thanks

Vikram

[Dr. Ozlem Ozbek]

Dear Vikram,

Thank you for eresponsing me. You can find my all calculations of  lnPD and deltaK graphs in xls file (1-5 pages) as well as bar plots as attached.