Why does STRUCTURE v2.3.4 (command line) does not work?
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11 weeks ago

I have been trying to run STRUCTURE on a small data set of 211 SNPs and 686 individuals. I have generated the input file using pgdspider and then removing the first line that specifies the name of the loci. I still get the same error that now I just do not understand.

There were errors in the input file (listed above). According to
"mainparams" the input file should contain  1372 rows with 213 entries .

There are 1372 rows of data in the input file, with an average of 213.00
entries per line.  The following shows the number of entries in each
line of the input file:

# Entries:   Line numbers
213:   1--1372
----------------------------------

Exiting the program due to error(s) listed above.


I do not understand this error. It looks like I my input file matches the specifics of the mainparams.txt (below)

#define INFILE paua_snps_outliers_structure_2.txt
#define OUTFILE paua_outliers_output
#define NUMINDS 686
#define NUMLOCI 211
#define LABEL 1
#define POPDATA 1
#define POPFLAG 0
#define PHENOTYPE 0
#define EXTRACOLS 0
#define PHASEINFO 0
#define MISSING -9
#define PLOIDY 2
#define ONEROWPERIND 0
#define GENENAMES 0
#define MAPDISTANCE 0
#define MAXPOPS 9
#define BURNIN 10000
#define NUMREPS 5


The command line I am using is the following

structure -m ./mainparams.txt -e ./extraparams.txt  -K 9 -L 211 -N 686 -i paua_snps_outliers_structure_2.txt


Can anyone help me please? I have noticed that this is a very common issue apparently but I have not found a way to solve it yet.

Thanks,

Giulia

STRUCTURE SNPs bash • 158 views