missing TemGenotypes.txt file after AftrRAD.pl run

[ninh...@gmail.com]

I tried out the example data and ran the AftrRAD.pl scripte with minDepth-3. All seems to work well, and I'm getting same output as shown in the AftrRAD_Example_README.txt file.

I then ran the Genotype.pl MinReads-3, but I got this error message

efgl@efgl:~/software/AftrRADv4.1$ perl Genotype.pl MinReads-3

Arguments entered are...

pvalThresh 100

MinReads 3

pvalLow 0.0001

pvalHigh 1e-05

Help 0

Running Genotype.pl...

Scoring genotypes at all nonparalogous loci.

Currently genotyping sample...OH_KLDR1006 sh: 1: R: not found

No such file or directory at Genotype.pl line 168.

I checked the code at line 168. It is trying to open TemGenotypes.txt file in the TempFiles directory, which does not exist.

Am I missing something obvious?

Best,

Ninh

[Mike Sovic]

Hi Ninh,

My first guess is that you don't have R installed, or it's not in your computer's path.  The point you're at in the AftrRAD pipeline is where R is called and used for the first time (line 163 of Genotypes.pl), and the output from running R here is the TempGenotypes.txt file.  You should be able to simply type 'R' at the command line prompt and the program should open.  If it doesn't, you'll need to get it installed in the path.  If necessary, you can download it from http://www.r-project.org.  Let us know if this doesn't fix the issue.

                    Mike  

[Ninh Vu]

FYI for others. I installed r and it works. Python and Perl come with Ubuntu (recent distros), but apparently not r.

Thanks

Ninh

[Mike Sovic]

Great - thanks for letting us know, Ninh.  

            Mike