fineRADstructure file error
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24 months ago
caranlove ▴ 10

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 • 651 views
Entering edit mode

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

Entering edit mode
9 weeks ago

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


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