StrAuto problem

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mz

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Jul 17, 2012, 12:28:02 AM7/17/12
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Hi,

I have tried your py scripts followed the manual. I succeed and got result for sim.str (example file). But when I test on my own data which has been used for Structure, I got error message below. 

Reading file "mainparams".
datafile is
ref13pop.str
Reading file "extraparams".
Note: RANDOMIZE is set to 1. The random number generator will be initialized using the system clock, ignoring any specified value of SEED.
Unable to open the file ref13pop.str.

All four files are in the same directory. My snp file is modified from .ped. This file was OK when I run Structure. Is it something particular with snp format. Does .str means .structure? I have tried to used program PGDSpider to convert .ped to .structure but it takes forever.

Any suggestion will be very helpful.
Best regards,

Vikram Chhatre

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Jul 17, 2012, 1:10:23 AM7/17/12
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Mz-

If you send me your data and parameter files (off the list), I will be happy to try them here. 

--------------------------------------------
Vikram Chhatre
Graduate Program in Genetics
Texas A&M University

Sent from my cell phone


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Adii_ (Institute of Genetics and Animal Breeding)

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Jul 17, 2012, 2:50:14 AM7/17/12
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Are You 100% sure, that the name of the file is OK? And STRUCTURE got rights to open it? 
In 99% this to reasons solve the issue :)

Best regards, 
Adii_ 

mz

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Jul 17, 2012, 3:50:52 AM7/17/12
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I think if the name of file was not correct, the error message might be “cannot find ref13pop.str”. What do you think?

 

Thank you very much for both of you. You are right, only one character is missing in the file name. I really looked at the file format.

 

Thanks again.

Mz

Vikram Chhatre

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Jul 17, 2012, 9:44:00 AM7/17/12
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mz -

Was your problem solved?

V
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