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Command used: wombat snappy5.par
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wombat snappy5.par
Script started on 2025-05-26 17:15:58+1000
 WOMBAT 26-05-2025 Maximum no. of threads to be used set to	      8

 Parameter file opened : "snappy5.par"
**RUNOP  --snap -v**
**COM Example14/E: GWAS with genetic groups**
**ANAL UNI**
  Analysis type = 1  "UNI"
  No. of traits =  1
**PEDS ../SimPed.dat**
  Pedigree file : "../SimPed.dat"
**DATA ../SimData.dat**
  Data file : "../SimData.dat"
**animal   0**
  Data - column :	 1  "animal"	     0
**kfix	   10**
  Data - column :	 2  "kfix"	  10
**mfix	   33**
  Data - column :	 3  "mfix"	  33
**kxl	  199**
  Data - column :	 4  "kxl"	199
**snp**
  Data - column :	 5  "snp"	 -1
**age**
  Data - column :	 6  "age"	 -1
**wgt**
  Data - column :	 7  "wgt"	 -1
**end**
**MODEL**
**COV  snp(1)**
**COV  age(2)**
**FIX  kfix**
**FIX  mfix**
**FIX  kxl**
**RAN animal  NRM**
**RAN gggrps  IDE**
**trait  wgt**
  Trait no.  1	"wgt"  Missing value  -123456789
**END MOD**
**VAR animal 1**
**30**
**VAR gggrps 1**
**10**
**VAR residual 1**
**70**
**SPECIAL**
**COVZER snp(1) FIT**
 Covariable:"snp(1)" Treat values of 0 as: FIT
**SNPEFF snp(1)**
**GENGROUPS gggrps 3 100**
 HACK_NUMBER GGRPS
 SPECIAL: Fit "explicit" genetic groups
 No. of groups given	       :	   3
 Scale factor for proportions  :   100.000000000000
 Random effect in model        : "gggrps"
**END**

 End of parameter file reached :  34 lines read
 "Animal" effect corresponding to genetic groups
 set to "animal" NRM
 Read genetic group proportions from pedigree file!
 Data file appers to be sorted correctly
 No. of records in total			   =	       16
 No. of animal IDs in data			   =	       16
 Routine "REDUCEPEDS" to eliminate animals not connected to the data
 -> this may not account properly for genotyped animals & their ancestors
    do not use this routine if you have such information - perform equivalent
    calculations yourself prior to running WOMBAT & use run option --norped
"../SimPed.dat": skipping first  2 lines
 No. of animal IDs in data			   =	       16
 ***Time: begin idvec			      0 	  0 Used since last	    0.2 	0.2
 ***Time: end idvec			      0 	  0 Used since last	    0.0 	0.0
 Expect to read genetic group proportions from pedigree file
 ->  column no.s	   5  to	   7
    (need "animal type" variable even if not required otherwise)
 Pedigree file					   = ../SimPed.dat
 Total no. of animal IDs found			   =	       26
 no. of NRM matrices		1	    1
 No. of "subjects" in data			   =	       16
 Maximum no. of records/individual =		   =		1	   399

 Inbreeding coefficients for random effect	   =		1 computed
 ... TIER's algorithm
 Covariance structure				   =	NRM
 No. of inbred animals				   =		0
 Average inbreeding coefficient 		   =  0.00000	  (in %)

 NRM Inverse no. :	     1	 "animal"
 No. of elements =	    66	 log determinant =  -11.0903548889591
    Zero out: 1st level  1  mfix	     1	 EqNo.	      7
    Zero out: 1st level  1  kxl 	     2	 EqNo.	     10
 No. of "subjects" in data			   =	       16
 No. of combinations of records 		   =		1
 No. of effect codes/ind. (maxnr)		   =		5
 Parameters to be estimated & their starting values
    1  COVS Z 1 1	    70.000000	  F
    2  COVS A 1 1	    30.000000	  F
    3  COVS B 1 1	    10.000000	  F
 LSQ: END data - nrczhz =	   57
 LSQ : additional dependency	      12   pivot -1.165734175856414E-015
 LSQ : additional dependency	      13   pivot  9.992007221626409E-016
 LSQ : additional dependency	      14   pivot -3.330669073875474E-016
 LSQ : additional dependency	      15   pivot  0.000000000000000E+000
 Coefficient matrix fixed effects - rank =     9  no. of rows =    15
    Zero Out	       1  Row/Columnn No.	    7
    Zero Out	       2  Row/Columnn No.	   10
    Zero Out	       3  Row/Columnn No.	   12
    Zero Out	       4  Row/Columnn No.	   13
    Zero Out	       5  Row/Columnn No.	   14
    Zero Out	       6  Row/Columnn No.	   15
 END "lsqfixed"
 No. of equations in full rank submatrix =	    38
 nq,neqns,nnginv	   1	      44	  66	       0  xx   3643.20000000000 	    3643  2147483646
 QTLSKIP	   1 eq no	     1
 No. of equations in full rank submatrix =	    37
 adjact ivcol	    32787	32787
 Elements in MMM - after data		      148
 Elements in MMM - after RE    1	      188
 Elements in MMM - after RE    2	      188
 Start of "GENMMD": no. of rows 		   =	       37
 End of "GENMMD": no of subscripts		   =	      172
 No. of equations in full rank submatrix =	    38
 adjact ivcol	    32787	32787
 Elements in MMM - after data		      175
 Elements in MMM - after RE    1	      215
 Elements in MMM - after RE    2	      215
 adjact ivcol	    32787	32787
 Elements in MMM - after RHS		      242
 End of "SMBFCT": maxsub			   =	      178	    39
		  maxlnz			   =	      287
		  nnops 			   =  1794.00	  0.100000E+16
 END "eqnorders"
 MAXLNZ 	287
node size =	    1 n =	  14
node size =	    2 n =	   4
node size =	    4 n =	   1
node size =	   13 n =	   1
 "Super-nodes" :  No. of nodes			   =	       20
		  Max. size			   =	       13
 NEW: Updated to allow for explicit genetic groups
 Start: factorisation of C  sys-time		   0.3
 End: factorisation of C  sys-time		 0.3
 Starting loop over SNPs ...
 File "SNPCounts.dat" found & opened
 Reading SNP allele counts with format: (16i1)
u =   17.751	se =   6.1679	  t =	2.8780	    SNPeffect1
u =  -6.6739	se =   7.5998	  t = -0.87816	    SNPeffect2
u =   11.582	se =   4.5552	  t =	2.5426	    SNPeffect3
u =   12.190	se =   5.0995	  t =	2.3904	    SNPeffect4

 "Snappy":	     4 cases for	    1  SNPs
 Output file for estimates: "SNPSolutions.dat"
 Total time used (secs): CPU =		 0  System =	       0
 Machine used = "didgeridoo"
 "WOMBAT" has finished !  26/05/2025


0.183u 0.211s 0:00.30 130.0%	0+0k 0+120io 0pf+0w

Script done on 2025-05-26 17:15:59+1000
