Running STRUCTURE from command line

Question

[giulia.trauzzi]

Hello,

I am trying to run STRUCTURE from the command line but I get the same error message (no of entries differs from the input file). Can anyone help me?

Here's the error message:

WARNING! Probable error in the input file.
Individual 686, locus 4954;  encountered the following data
" when expecting an integer

readlociEOF


WARNING:  Unexpected end of input file.  The details of the
input file are set in mainparams.  I ran out of data while reading
the data for individual 686.

----------------------------------
There were errors in the input file (listed above). According to
"mainparams" the input file should contain one row of markernames with 7698 entries,
 1372 rows with 7701 entries .

There are 1373 rows of data in the input file, with an average of 7700.00
entries per line.  The following shows the number of entries in each
line of the input file:

# Entries:   Line numbers
     7698:   1
     7700:   2--1373
----------------------------------

Exiting the program due to error(s) listed above

And here's my mainparam file

#define MAXPOPS 10 "int"
#define BURNIN 10000 "int"
#define NUMREPS 100000 "int"
#define INFILE pauapop_structure.txt "str"
#define OUTFILE structure_out "str"
#define NUMINDS 686 "int"
#define NUMLOCI 7698 "int"
#define PLOIDY 2 "int"
#define MISSING 0 "int"
#define LABEL 1 "int"
#define LOCDATA 1 "int"
#define POPDATA 9 "int"
#define POPFLAG 0 "int"
#define EXTRACOLS 1 "int"
#define PHENOTYPE 0 "int"
#define MARKERNAMES 1 "int"

And the extraparam file

#define NOADMIX 0 "int"
#define LOCPRIOR 1 "int"

Thanks to whoever will be able to help me

Giulia

[4galaxy77]

Can you post the error message you are getting and the full command line arguments as well?

Answer 1

[Arthur]

If it cans help, I got the same error message :

There were errors in the input file (listed above). According to "mainparams" the input file should contain one row of markernames with XXX entries, XXX rows with XXX entries . There are XXX rows of data in the input file, with an average of XXX.00 entries per line. The following shows the number of entries in each line of the input file

After hours of editing my files, I discovered that STRUCTURE requires populations to be labeled with integer numbers only. Probably the same for individuals? It worked for me after changing my individual and population names (for example : pop123 -> 123)