fineRADstructure file error
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4.4 years ago
Whirlingdaf ▴ 40

Hi all, I am working with fineradstructure for the first time and am encountering an error that I am having issues solving.

I have successfully run the first command:

   /RADpainter paint stacks_finerad_min4.finerad

This ran fine and also gave me a list of samples which have a lot of missing data. So I went ahead and removed these particular samples from the finerad file and am now attempting to run the next finestructure step to identify popualtions:

./finestructure -x 100000 -y 100000 -z 1000 stacks_finerad_min4_chunks.out INPUT_RAD_FILE_chunks.mcmc.xml

However, this gives me the error:

Invalid file!

So, I went back and tried the original file, with all samples included, and I get the same result. A small example of what my input file looks like is:

#Cfactor 0.316101
Recipient M1280_P4 M1281_P4 M1310_P4 M1311_P4 M1312_P4 M1314_P4 M1271_P6 M1280_P4 0 14.9906 14.9275 15.0751 15.3868 14.617 14.8028 M1281_P4 15.7998 0 15.6526 15.3866 15.8445 15.6611 15.7681 M1310_P4 15.4973 15.4236 0 18.1855 15.7372 15.4389 15.5581

Any suggestions on what could be going wrong? Thanks for the help!

finestructure fineradstucture structure SNP RADseq • 1.3k views
Entering edit mode

I'm having this same issue! Did you ever figure out what the error means?

Entering edit mode
2.6 years ago

I'm having this same issue! Did you ever figure out what the error means?


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