Clumpp error

[Heather]

Hi all. I am running into some issues using CLUMPP (v. 1.1.2) and I
was hoping I could get some help. I used Structure Harvester on my
zipped Structure (v. 2.3.3) output to generate the popfiles needed for
CLUMPP. Do I need to modify the popfile exported by Structure
Harvester before using it in CLUMPP? I keep getting an error message
"Premature end of popfile. Note: This problem could also be caused
by giving any of the parameters R, K and C the wrong number." I'm
certain that I've correctly defined R, K, and C--what am I doing
wrong? Thanks!

[Vikram Chhatre]

Hi Heather:

For CLUMPP analysis, you will need to first choose whether you want to
choose to cluster populations or individuals. If individuals, you can
use the K*.indfile generated by Harvester. This indfile should
contain data for all the runs you did for that particular K value. So
essentially, based on Harvester output plots, you should decide upon
what is the most optimal number of clusters in your data and choose
the corresponding indfile only for the analysis.

The name of this indfile should be written to the clumpp parameter
file. The datatype for clumpp in this case will be 0 (it would have
been 1 if you were to use popfile).

Other settings in the parameter file are self explanatory. As for the
algorithm to use, "full search" takes a really long time. The greedy
and largeKgreedy aren't as accurate but are much faster.

So to answer your question, you do not need popfile, if your focus is
clustering of individuals.

If you're still getting errors, I will be more than happy to look at
your files (off the list).

HTH
Vikram

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[Julie Hebert]

My first guess is to make sure your input files all look like the one
in the manual (parentheses, colons, the works). Even though the manual
says the extra columns don't matter, if they aren't formatted exactly
right, it won't work. (For example, if it is looking for a
parentheses, and you don't have any, it might think it only has one
value in one column.)
I hope that helps!
Julie

[Verónica Arenas]

Hi!

I've the same problem, I did the .indfile run and have no problems with that. 

But when I try to do the .popfile run, an error message appears on the screen and

cannot continue with the software.

Plase help!

Thanks!!

[Vikram Chhatre]

Can you show us your files?  Attach them to your reply as a zip archive.

V

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[Anna Tigano]

Hi,
I'm having the same problem with the popfile.
The indfile has no problem, either copying and pasting from the Structure output or from Structure Harvester. But I can't make CLUMPP run with any popfile.
I'm working on a Mac, if that makes any difference.
Thanks in advance
Anna

[Vikram Chhatre]

Please post your ind, pop and parameter files as a zip archive.

[Anna Tigano]

A friend helped me figuring it out!
The error was in C, which I didn't change switching from individuals to populations.
Thank you very much anyway.
And for the others, there is nothing wrong with Structure Harvester output...

[Jackie]

Many thanks to Anna Tigano for posting the above note, helped me to troubleshoot!

On Monday, March 30, 2015 at 4:45:19 PM UTC-4, Anna Tigano wrote:

A friend helped me figuring it out!
The error was in C, which I didn't change switching from individuals to populations.
Thank you very much anyway.
And for the others, there is nothing wrong with Structure Harvester output...

On Monday, March 30, 2015 at 4:08:50 PM UTC-4, Vikram Chhatre wrote:
> Please post your ind, pop and parameter files as a zip archive.
>
>
> On Mon, Mar 30, 2015 at 4:07 PM, Anna Tigano <annat...@gmail.com> wrote:
> Hi,
>
> I'm having the same problem with the popfile.
>
> The indfile has no problem, either copying and pasting from the Structure output or from Structure Harvester. But I can't make CLUMPP run with any popfile.
>
> I'm working on a Mac, if that makes any difference.
>
> Thanks in advance
>
> Anna
>
>
>
>
>
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[Ting]

Dear all,

I am a new user to the Software Structure Harvester and CLUMPP (win_v1.1.2b). When I used the popfile generated from the Structure Harvester, there came the same error message.

Error: Premature end of popfile ''K2.popfile''.

Note: This problem could also be caused by giving any of the parameters R, K and C the wrong number.

However, I'm sure that I've correctly defined all the three parameters (R, K, and C). I feel confused and have difficulty in figuring out what is really wrong. Could anyone give me some suggestions?

Thank you very much for your time and your kind help! :D

Best regards,
Ting