Re: [structure-group] CLUMPP help - unable to read paramfile or indfile??

[Vikram Chhatre]

Hazel -

It would be hard to suggest anything without more information.  If you'd like send a zip archive of all your files off the list and I will try to run it here.

V

On Wed, Jan 30, 2013 at 11:52 AM, Hazel Jackson <hazelja...@yahoo.co.uk> wrote:

I've been trying to use Clumpp on a MAC but cannot get it to run.  I've saved the K*.indfile from structure harvester, and adapted one of the example paramfiles from the download folder.  When I try to run Clumpp it says it cannot read the paramfile...

I have changed the relevant parts of the paramfile (ie, data = 0, name of indfile etc..)

Any ideas would be gratefully recieved.

Thanks all

Hazel

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[Hazel Jackson]

Hi

Apologies for my delayed reply.  That would be great, I've attached the compressed files.  I'm sure it'll be something simple! Once again, many thanks

Hazel

On Wednesday, 30 January 2013 17:57:27 UTC, Vikram Chhatre wrote:

Hazel -

It would be hard to suggest anything without more information.  If you'd like send a zip archive of all your files off the list and I will try to run it here.

V

On Wed, Jan 30, 2013 at 11:52 AM, Hazel Jackson <hazelja...@yahoo.co.uk> wrote:

I've been trying to use Clumpp on a MAC but cannot get it to run.  I've saved the K*.indfile from structure harvester, and adapted one of the example paramfiles from the download folder.  When I try to run Clumpp it says it cannot read the paramfile...

I have changed the relevant parts of the paramfile (ie, data = 0, name of indfile etc..)

Any ideas would be gratefully recieved.

Thanks all

Hazel

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[Vikram Chhatre]

There were a few problems:

1. The paramfile.txt is not a valid name, unless you tell CLUMPP that name of parameter file has a txt extension.  

2. If you use LargeKGreedy algorithm, that takes a long time (at least in my experience) to permute 

3. I changed the method to Greedy and the # of repeats to 1000

The results archive is attached.  Note that you will have to run analogous analysis for population popfile.  Then use the resulting ind and pop outfiles with Distruct.

V

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[Hazel Jackson]

Ahh how odd, on my MAC it doesn't show as having a .txt extension.

Thats brilliant, thank you for your help! Much appreciated.

Best wishes

Hazel

On Thursday, 31 January 2013 13:52:16 UTC, Vikram Chhatre wrote:

There were a few problems:

1. The paramfile.txt is not a valid name, unless you tell CLUMPP that name of parameter file has a txt extension.  

2. If you use LargeKGreedy algorithm, that takes a long time (at least in my experience) to permute 

3. I changed the method to Greedy and the # of repeats to 1000

The results archive is attached.  Note that you will have to run analogous analysis for population popfile.  Then use the resulting ind and pop outfiles with Distruct.

V

On Thu, Jan 31, 2013 at 6:18 AM, Hazel Jackson <hazelja...@yahoo.co.uk> wrote:

Hi

Apologies for my delayed reply.  That would be great, I've attached the compressed files.  I'm sure it'll be something simple! Once again, many thanks

Hazel

On Wednesday, 30 January 2013 17:57:27 UTC, Vikram Chhatre wrote:

Hazel -

It would be hard to suggest anything without more information.  If you'd like send a zip archive of all your files off the list and I will try to run it here.

V

On Wed, Jan 30, 2013 at 11:52 AM, Hazel Jackson <hazelja...@yahoo.co.uk> wrote:

I've been trying to use Clumpp on a MAC but cannot get it to run.  I've saved the K*.indfile from structure harvester, and adapted one of the example paramfiles from the download folder.  When I try to run Clumpp it says it cannot read the paramfile...

I have changed the relevant parts of the paramfile (ie, data = 0, name of indfile etc..)

Any ideas would be gratefully recieved.

Thanks all

Hazel

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[Vikram Chhatre]

Yes, sometimes Mac, even after deleting the extension, simply hides it.  I had to use the 'mv' command in terminal.

All the best

V

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[Hazel Jackson]

Sorry V, I'm having another problem

I understand I should be getting the popq file from my structure harvester output but no luck.  I've been looking on the forum but can't figure out what i'm doing wrong again.

any tips...?

Thanks AGAIN

Hazel

[Vikram Chhatre]

.popfile looks like .indfile, except that it shows memberships in respective clusters for populations, not individuals.  See below for an example.  The last column is number of individuals in each population.

V

1:     0.486  0.514 41

 2:     0.514  0.486 14

 3:     0.535  0.465 10

 4:     0.529  0.471 80

 

 1:     0.514  0.486 41

 2:     0.485  0.515 14

 3:     0.464  0.536 10

 4:     0.471  0.529 80

 

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[Hazel Jackson]

Ah right ok, i've been through all the files output by structure harvester and i don't get anything like that.

Do you think it could be something wrong with the way I've run structure?

Thank you!

Hazel

[Vikram Chhatre]

Search for a thread by 'Caroline Duffie' on the list archive.  Your answer might be in there.

V

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[Hazel Jackson]

PERFECT!! It seems my original input file was slightly incorrect (I had an extra two tabs on the first line).

Problems sorted.

Thanks again for all your help!

Hazel

[Hazel Jackson]

Hi again

I'm SO FRUSTRATED.  I just cannot get the program to work on my MAC.  Everytime i try i get an error message that it cannot read the paramfile.  V, I have tried running the files you did for me and those won't work either.  I notice you mentioned you used some command in terminal.  Can you help here? I attach the files again.  I cannot find that the paramfile has a txt extension as you found last time either? I'm really stumped again and can't understand why i'm having such trouble with this.

Many thanks

Hazel

[Vikram Chhatre]

I havent looked at your files yet, but make sure the paramfile is readable. Try the following in a terminal. 

chmod +rw paramfile 

V

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[Vikram Chhatre]

Hazel -

Your paramfile is named K2.paramfile.  No wonder the program cannot see it.  You can change the name of the paramfile, but then you have to explicitly call for it, e.g.

./CLUMPP K2.paramfile

V

[Hazel Jackson]

Hi

I have tried with just the file called paramfile and this doesn't work either. I tried changing the name to k2.paramfile to see if that would help (after looking at the download examples). 

Sent from my iPhone

[Julie Hebert]

Hazel,

I noticed your "POPFILE" did not have a "#" before it. If you're working with individuals instead of populations, you can put a # in front of the POPFILE to make it text instead of a command. Likewise, if you're running populations, change the INDFILE to a comment by putting a # in front of it and remove the # in front of the POPFILE. Once I did that, I was able to run CLUMPP on your data. I'm attaching the files.

Julie

V

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[Junli Zhang]

Hi Hazel,

I downloaded your data, and tried running CLUMPP in my Ubuntu 12.10. I have CLUMPP installed in my machine. So I tried "clumpp K2.paramfile", it worked. If I changed "K2.paramfile" to "paramfile", then just ran "clumpp" without any parameters, it also worked. So the content of the "paramfile" or the file name should be not a problem. Attached is a output file from your data.

I do not have a Mac and I never used a Mac. But I know it is also a Unix system. So you can try: 1) check whether file "paramfile" is readable (as suggested by Vikram); 2) 'save as' the "paramfile" as a Mac text file format and encoding; 3) recompile the CLUMPP on your Mac. Hope it helps. Good luck.

Junli

On Wed, Feb 6, 2013 at 6:50 AM, dwhr <dwh...@gmail.com> wrote:

Hi Hazel,
I've been having the same issue - no matter the file name and/or extension, I can't get CLUMPP to take mt paramfile.  But, when I transferred to a PC it started right up.  This was exciting, until it told me I had 2billion permutations to test and was still "running" after three days.  Time will tell?
Dan

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[Julie Hebert]

One more note: in general, I suggest running both CLUMPP and distruct using the command line (via terminal or cmd depending on your operating system). If you just double click on the program, it closes before you can get any errors, so you can't trouble shoot why it is not working.

Julie

[Julie Hebert]

Following up on Hazel's problem a while back. I'm working with someone trying to run CLUMPP on a mac (and I've tried it on a mac in my lab as well) and we can't get it to run. There is no extension (hidden or otherwise) on the paramfile, and I've made sure the permissions are correct. I get the same error message: 

Error: Unable to open paramfile ' ' paramfile ' '

Please check the  name of the paramfile.

So, has anyone figured out how to get this to run? (I even tried running the original version, freshly downloaded.)

Julie

[Julie Hebert]

Nevermind. I figured it out: for those of you who don't use macs regularly (like myself) apparently CLUMPP won't run if you use the typical double click or typing "open CLUMPP" in terminal. However, if you type "./CLUMPP" in terminal, it works just fine.

grumble. :)

Julie

[D Israel]

Thanks everyone.  I am new at this and all of the comments were helpful!

[Maya]

Hi,

I am having problems running CLUMPP on my Mac. I use Mountain Lion (OSX v 10.8.4).

The paramfile reads fine, but there seems to be a problem with the Structure Harvester output files I am using.

When I try to run my indfile, I get the following error:

Running...
----------------------------------
Best estimate of H' Repeat number (of 100)
Bus error: 10

When I try to run the popfile, I get the following error:

Error: Premature end of popfile ''K5.popfile''

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

However, I already checked the number of R, K and C and it is correct on the paramfile. Any thoughts?

Files are attached...

Thanks in advance,
Maya

[Vikram Chhatre]

Maya -

Feel free to send the files to me off the list.  I will be happy to take a look.

V

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[Laura Tensen]

Op woensdag 30 januari 2013 19:52:20 UTC+2 schreef Hazel Jackson:

> I've been trying to use Clumpp on a MAC but cannot get it to run. I've saved the K*.indfile from structure harvester, and adapted one of the example paramfiles from the download folder. When I try to run Clumpp it says it cannot read the paramfile...
>
> I have changed the relevant parts of the paramfile (ie, data = 0, name of indfile etc..)
>
> Any ideas would be gratefully recieved.
>
> Thanks all
>
> Hazel

Hi Vikram and co.,

Are you still active in saving lost CLUMPP souls? Ive read the whole manual and discussion and though useful, none of the changes I applied make any difference.. the program still wont read my paramfile. Can I maybe send the paramfile to anyone?

Thanks a lot!

Cheers Laura

[Vikram Chhatre]

Hi Laura,

What is the error message you are receiving?  Make sure that your paramfile isn't actually paramfile.txt.  Sometimes on Apple computers, Finder does not show filename extensions.

V

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[Laura Tensen]

Hi Vikram,

 

I tried to make sure its not a txt extension and checked. Im working on windows as well

 

All the best,

 

Laura

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[Vikram Chhatre]

What is the error message?