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Command used: wombat snappy.par
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wombat snappy.par
Script started on 2025-05-26 17:15:57+1000
 WOMBAT 26-05-2025 Maximum no. of threads to be used set to	      8

 Parameter file opened : "snappy.par"
**RUNOP  --snap -v**
**COM Example14/A: Simple univariate GWAS**
**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**
**trait  wgt**
  Trait no.  1	"wgt"  Missing value  -123456789
**END MOD**
**VAR animal 1**
**30**
**VAR residual 1**
**70**
**SPECIAL**
**COVZER snp(1) FIT**
 Covariable:"snp(1)" Treat values of 0 as: FIT
**SNPEFF snp(1)**
**END**

 End of parameter file reached :  30 lines read
 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
 Pedigree file					   = ../SimPed.dat
 Total no. of animal IDs found			   =	       26
 no. of NRM matrices		1	    1
 Pruned pedigree for random effect no.		 1
 Original no. of animals =	    26
 New no. of animals	 =	    26
 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 %)

 File "PrunedPedFile1.dat" written
 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)		   =		4
 Parameters to be estimated & their starting values
    1  COVS Z 1 1	    70.000000	  F
    2  COVS A 1 1	    30.000000	  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 =	    35
 nq,neqns,nnginv	   1	      41	  66  xx   2838.00000000000		2838  2147483646
 QTLSKIP	   1 eq no	     1
 No. of equations in full rank submatrix =	    34
 adjact ivcol	    25542	25542
 Elements in MMM - after data		       83
 Elements in MMM - after RE    1	      123
 Start of "GENMMD": no. of rows 		   =	       34
 End of "GENMMD": no of subscripts		   =	      123
 No. of equations in full rank submatrix =	    35
 adjact ivcol	    25542	25542
 Elements in MMM - after data		      107
 Elements in MMM - after RE    1	      147
 adjact ivcol	    25542	25542
 Elements in MMM - after RHS		      171
 End of "SMBFCT": maxsub			   =	      135	    36
		  maxlnz			   =	      211
		  nnops 			   =  1079.00	  0.100000E+16
 END "eqnorders"
 MAXLNZ 	211
node size =	    1 n =	  12
node size =	    2 n =	   5
node size =	    4 n =	   1
node size =	   10 n =	   1
 "Super-nodes" :  No. of nodes			   =	       19
		  Max. size			   =	       10
 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 =   17.795	se =   6.1267	  t =	2.9046	    SNPeffect1
u =  -6.6739	se =   7.5998	  t = -0.87816	    SNPeffect2
u =   11.614	se =   4.5143	  t =	2.5728	    SNPeffect3
u =   12.160	se =   5.0989	  t =	2.3848	    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


0.207u 0.174s 0:00.29 127.5%	0+0k 0+120io 0pf+0w

Script done on 2025-05-26 17:15:57+1000
