CLUMPP error indfile

[Jennifer Day]

I see by reading other posts to the group that the "Error: Unable to read value in indfile ...." is common, and the usual problem is incorrectly specifying R, K, or C.  

I've double checked my parameter inputs and .indfile (an expected RxC number of rows, plus some blank rows which should not be a problem, and K=2 + 5 columns) - and so I'm stumped.  I hope this isn't a simple oversight on my part.  

I followed the guidelines on the Population Genetics Notes blog to generate my .indfiles and used the example paramfile as a template. I'm running CLUMPP.exe (for Windows 1.1.2) from the folder in which these two files exist (using GitBash).

[Vikram Chhatre]

You need a parenthesis around values in column 3.  

In vim:

:%s/ \([1-9]\) 1 :/ \(\1\) 1 :/g

Then try again.

V

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[Jennifer Day]

Thanks!  Adding the parentheses got me through the .indfile error - and the program seems to reading in the parameter file correctly

However, once it starts to run, it crashes, no output files created.

[Vikram Chhatre]

I was hoping you wouldn't get the core dumped error that I was getting too. 

Compare your file with example data to see if you can find any abnormalities. 

V

[Jennifer Day]

I don't see any differences between the formatting of the example chicken.indfile and my K2.indfile.  I'm using Notepad++ as my text editor and saving my .indfile as a "normal text file", but I don't think that's adding any hidden formatting.  Does the .indfile need to be tab delimited?

On Friday, September 11, 2015 at 9:26:16 AM UTC-7, Jennifer Day wrote:

[Vikram Chhatre]

Yeah I would try tab delim. 

V

On Friday, September 11, 2015, Jennifer Day <jenma...@gmail.com> wrote:

[Jennifer Day]

Changed spaces to tabs.  No luck.

On Friday, September 11, 2015 at 9:26:16 AM UTC-7, Jennifer Day wrote:

[Vikram Chhatre]

Did you change the W and S parameters from their default values?  When I used a default settings paramfile with your data, there were no errors.

[Vikram Chhatre]

It's been a while since I delved into CLUMPP.  First, try running the example dataset that comes with the program.  If it runs correctly, compare formatting of example data with your own.  If you are still not sure what's wrong, feel free to post your files here and someone will help you.

V

On Thu, Sep 28, 2017 at 2:10 AM, Christian Robiso <christi...@gmail.com> wrote:

Hello V. and company,

Are you still active on helping lost souls in CLUMPP/Distruct?

I am also having trouble with my CLUMPP run. I'm pretty sure I have the right input since I just transferred my indfile run from Structure without any changes.

My command line says:

Error: Unable to read value in indfile "K3.indfile"
Please check the indfile and the value at row 1821 and column 1.

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

I hope you can help me on this.

Thanks!
Christian

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[Vikram Chhatre]

Christian,

Can you confirm that you have run the test data set and it works fine?

V

On Thu, Sep 28, 2017 at 8:11 AM, Christian Robiso <christi...@gmail.com> wrote:

Alright. I accidentally stumbled upon this group while I was searching on how to make CLUMPP work. I have followed the instructions from the software re: its data format and I think I have already done it right (I hope I am not overlooking something), but I am still not able to run CLUMPP. Here is the zip file for my indfile with a screenshot of the error that I am receiving from CLUMPP. I hope someone can help me. Thanks a lot in advance! 

On Thursday, September 28, 2017 at 9:17:26 PM UTC+8, Vikram Chhatre wrote:

It's been a while since I delved into CLUMPP.  First, try running the example dataset that comes with the program.  If it runs correctly, compare formatting of example data with your own.  If you are still not sure what's wrong, feel free to post your files here and someone will help you.

V

On Thu, Sep 28, 2017 at 2:10 AM, Christian Robiso <christi...@gmail.com> wrote:

Hello V. and company,

Are you still active on helping lost souls in CLUMPP/Distruct?

I am also having trouble with my CLUMPP run. I'm pretty sure I have the right input since I just transferred my indfile run from Structure without any changes.

My command line says:

Error: Unable to read value in indfile "K3.indfile"
Please check the indfile and the value at row 1821 and column 1.

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

I hope you can help me on this.

Thanks!
Christian

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[Vikram Chhatre]

Number of runs should be 10, not 100.

On Thu, Sep 28, 2017 at 8:32 AM, Christian Robiso <christi...@gmail.com> wrote:

Yes, here is a screenshot of an ongoing run using the sample data set from CLUMPP. I think I have already made the necessary changes for my indfile, but it won't still run.

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Christian John S. Robiso

Science Research Specialist II

Plant Molecular Genetics Laboratory

Institute of Biology | Philippine Genome Center

University of the Philippines
Diliman, Quezon City, 1101
Philippines

Telephone: (02) 981-8500 loc 3735

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