[structure-group] Can't open the file "mainparams"

[Consuelo]

Hello folks,

I'm trying to run Structure 2.2 in a Debian machine but I got this
error: Can't open the file "mainparams".
I have created and exported the mainparams with the Windows version
(v3.3 though). However, all the parameters started with #define. Since
it didn't work, I remove the #define part, thinking they could be
understood as comments. But it didn't work anyways...

Here is the file, I hope someone can give me a hand!!! Thanks!

OUTFILE /home/consuelo/structure/out/results.txt
INFILE /home/consuelo/structure/input/project_data
NUMINDS 75
NUMLOCI 321
LABEL 1
POPDATA 1
POPFLAG 0
LOCDATA 0
PHENOTYPE 0
MARKERNAMES 0
MAPDISTANCES 0
ONEROWPERIND 0
PHASEINFO 0
PHASED 0
RECESSIVEALLELES 0
EXTRACOLS 0
MISSING -9
PLOIDY 2
MAXPOPS 2
BURNIN 50000
NUMREPS 100000
LINKAGE 0
NOADMIX 1
ADMBURNIN 25000
USEPOPINFO 0

LOCPRIOR 0

FREQSCORR 0


INFERLAMBDA 1
POPSPECIFICLAMBDA 0
LAMBDA 1.0
COMPUTEPROB 1
PFROMPOPFLAGONLY 0
ANCESTDIST 0
STARTATPOPINFO 0
METROFREQ 10


UPDATEFREQ 1

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[Thirsa-K]

Hi Consuelo,

Since you say that you're trying to open this mainparams file in
version 2.2 of Structure, there might be a very simple reason for your
problem: Version 2.2 did not yet have the "use sampling locations as
prior" option, which is present in version 2.3 an up.
So.....possibly....the program simply doesn't understand the commands
related to that option (LOCDATA 0 and LOCPRIOR 0).

Below is a print of one of my mainparams files from version 2.2 of
Structure. As you can see, there are some other differences compared
to your file. So.....if you adjust the set-up of your mainparams file
to the set-up below......maybe it will work......

#define OUTFILE C:\Statistics\Structure2.2\SNPs\Results\admix-
correl_run_1
#define INFILE C:\Statistics\Structure2.2\SNPs\SNPs-zonder-popinfo
\project_data
#define NUMINDS 2818
#define NUMLOCI 13
#define LABEL 1
#define POPDATA 1
#define POPFLAG 0
#define PHENOTYPE 0
#define MARKERNAMES 0
#define MAPDISTANCES 0
#define ONEROWPERIND 1
#define PHASEINFO 0
#define PHASED 0
#define RECESSIVEALLELES 0
#define EXTRACOLS 0
#define MISSING -9
#define PLOIDY 2
#define MAXPOPS 7
#define BURNIN 10000
#define NUMREPS 20000


#define NOADMIX 0
#define LINKAGE 0
#define USEPOPINFO 0
#define INFERALPHA 1
#define ALPHA 1.0
#define POPALPHAS 0
#define UNIFPRIORALPHA 1
#define ALPHAMAX 10.0
#define ALPHAPROPSD 0.025


#define FREQSCORR 1
#define ONEFST 0
#define FPRIORMEAN 0.01
#define FPRIORSD 0.05


#define INFERLAMBDA 0
#define LAMBDA 1.0
#define COMPUTEPROB 1
#define PFROMPOPFLAGONLY 0
#define ANCESTDIST 0
#define STARTATPOPINFO 0
#define METROFREQ 10


#define UPDATEFREQ 1

Good luck,
Thirsa

[Consuelo]

ok!! I'll try that!! thanks!!

[Thirsa-K]

Just curious......did it work?