R error message

[jmwhi...@mix.wvu.edu]

I am attempting to run AftrRAD with demultiplexed data. I got through the first step, but when I ran perl Genotype.pl, I got the error message below. R is installed and functioning properly (I think). I can pull it up from the shortcut and the terminal. I recognize the R error "subscript out of bounds," and I am assuming there is a problem in one of my output files from the first step, but am unsure of how to correct the problem. Is it something that needs to be fixed prior to running perl AftrRAD.pl, or is it something that I can fix in the output file itself? Or, does the script need to be adjusted for my output? Any help would be much appreciated! 

Currently genotyping sample...Afu-Mig-01_S23_L001_R1_001 Error in GenotypesMatrix[CurrentSecondRow, 2] : subscript out of bounds

Execution halted

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

Thanks!

[Mike Sovic]

Yep - I expect you're right that the problem is associated with one of the output files from the first step.  We'll work backwards in terms of some of the output files that should be created, and see if we can track down the issue.  Check the following…

1.)  In the TempFiles directory, there should be a series of files named 'ForBinomialTestX.txt', where 'X' is one of your sample names.  Open these  and make sure they contain data (should contain all of the polymorphic loci, along with read counts for that sample).

2.)  In the Output/PolymorphicLoci directory, there should be a large number of relatively small text files named 'CandidateLocusX.txt'.  Each contains one polymorphic locus that was identified.

3.)  In the TempFiles/ErrorReadTest directory, there should be a file 'ErrorTestOut.txt' that contains a large number of sequence reads.

Let us know if you have each of these files, and if they appear to contain data as they should, and we'll go from there.

           Mike