individual 1164 has negative location! locations should be >= 0, I know this is a common problem but I can't seem to resolve it!

[Edward Myers]

Hey all, I know this has come up in the past but I don't know where the error is in my file. I have changed the POPDATA, USEPOPINFO, etc. to =0 but continue to get the error that 'individual 1164 has negative location! locations should be >= 0' (individual 1164 is the first individual in my infile). I do not have location information in my infile just locus information. Below is my parameter file, any input/suggestions are welcome!

KEY PARAMETERS FOR THE PROGRAM structure. YOU WILL NEED TO SET THESE
IN ORDER TO RUN THE PROGRAM. VARIOUS OPTIONS CAN BE ADJUSTED IN THE
FILE extraparams.


"(int)" means that this takes an integer value.
"(B)" means that this variable is Boolean
(ie insert 1 for True, and 0 for False)
"(str)" means that this is a string (but not enclosed in quotes!)


Basic Program Parameters

#define MAXPOPS 2 // (int) number of populations assumed
#define BURNIN 100 // (int) length of burnin period
#define NUMREPS 200 // (int) number of MCMC reps after burnin

Input/Output files

#define INFILE get_test // (str) name of input data file
#define OUTFILE outfile_get //(str) name of output data file

Data file format

#define NUMINDS 10 // (int) number of diploid individuals in data file
#define NUMLOCI 7 // (int) number of loci in data file
#define PLOIDY 2 // (int) ploidy of data
#define MISSING -9 // (int) value given to missing genotype data
#define ONEROWPERIND 0 // (B) store data for individuals in a single line


#define LABEL 1 // (B) Input file contains individual labels
#define POPDATA 0 // (B) Input file contains a population identifier
#define POPFLAG 0 // (B) Input file contains a flag which says
whether to use popinfo when USEPOPINFO==0
#define LOCDATA 0 // (B) Input file contains a location identifier

#define PHENOTYPE 0 // (B) Input file contains phenotype information
#define EXTRACOLS 0 // (int) Number of additional columns of data
before the genotype data start.

#define MARKERNAMES 0 // (B) data file contains row of marker names
#define RECESSIVEALLELES 0 // (B) data file contains dominant markers (eg AFLPs)
// and a row to indicate which alleles are recessive
#define MAPDISTANCES 0 // (B) data file contains row of map distances
// between loci


Advanced data file options

#define PHASED 0 // (B) Data are in correct phase (relevant for linkage model only)
#define PHASEINFO 0 // (B) the data for each individual contains a line
indicating phase (linkage model)
#define MARKOVPHASE 0 // (B) the phase info follows a Markov model.
#define NOTAMBIGUOUS -999 // (int) for use in some analyses of polyploid data



Command line options:

-m mainparams
-e extraparams
-s stratparams
-K MAXPOPS
-L NUMLOCI
-N NUMINDS
-i input file
-o output file
-D SEED



Thanks!!!

[Vikram Chhatre]

Given your parameters, every individual should have two rows of data, one allele on each line.  There should be 8 columns of data (1 for label, 7 for loci).  Make sure the end of line character is set properly for the operating system in use.

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[Edward Myers]

Hey Vikram,
Thanks for the reply. That is how the infile is set up, where each individual has two lines and there are 8 columns as you describe. This is just a subset of my data, that I wanted to run as a test. I can run the program with the example file no problem, I just run into this error with my own data. Any other thoughts?
Ed

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[Vikram Chhatre]

If you email me the files directly, I would be glad to take a look.  Please send mainparams and infile.

V

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[Brett Addis]

Was there a solution to this problem?  I am experiencing the same thing, despite setting POPDATA and USEPOPINFO to 0.

Thanks,

Brett

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