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Command used: wombat s1step2.par
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wombat s1step2.par
Script started on 2025-05-26 17:25:31+1000
 WOMBAT 26-05-2025 Maximum no. of threads to be used set to	      8

 Parameter file opened : "s1step2.par"
**RUNOP -v --s1step**
**COM Example 18/B: Bivariate S1STEP analysis; mouse data from Example 2**
**ANAL MUV 2**
  Analysis type = 2  "MUV 2"
  No. of traits =  2
**DATA ../muwex2.d**
  Data file : "../muwex2.d"
**tr1 traitno 2**
  Data - column :	 1  "traitno"	      2
**tr1  animal 555**
  Data - column :	 2  "animal"	   555
**tr1  sire**
  Data - column :	 3  "sire"	  -1
**tr1  dam**
  Data - column :	 4  "dam"	 -1
**tr1  generation 4**
  Data - column :	 5  "generation"	 4
**tr1  sex	  2**
  Data - column :	 6  "sex"	  2
**tr1  littersize 7**
  Data - column :	 7  "littersize"	 7
**tr1  litterno   55**
  Data - column :	 8  "litterno"	      55
**tr1	weight	 0**
  Data - column :	 9  "weight"	     0
**tr2  traitno 2**
  Data - column :	 1  "traitno"	      2
**tr2  animal 555**
  Data - column :	 2  "animal"	   555
**tr2  sire**
  Data - column :	 3  "sire"	  -1
**tr2  dam**
  Data - column :	 4  "dam"	 -1
**tr2  generation 4**
  Data - column :	 5  "generation"	 4
**tr2  sex	  2**
  Data - column :	 6  "sex"	  2
**tr2  littersize 7**
  Data - column :	 7  "littersize"	 7
**tr2  litterno   55**
  Data - column :	 8  "litterno"	      55
**tr2  fintake	 0**
  Data - column :	 9  "fintake"	      0
**END**
**MODEL**
**FIX generation**
**FIX sex**
**FIX littersize**
**SUBJ animal**
**RAN animal  GIN**
**ran litterno**
**trait weight 1**
  Trait no.  1	"weight"  Missing value  -123456789
**tr  fintake  2**
  Trait no.  2	"fintake"  Missing value  -123456789
**END MOD**
**VAR animal 2 2**
**4.9 1.0 6.0**
**VAR litterno 2 2**
**1.5  1.0 3.0**
**VAR residual 2 2**
**1.7  1.0  12.6**

 End of parameter file reached :  39 lines read
  skipping check for sorting of data
 No. of "subjects" in data			   =	      284
 Maximum no. of records/individual =		   =		2	   399
 File						   = "animal.gin"
 No. of records 				   =	     1014
 Denseness of matrix				   =  1.75950	 %
 No. of diagonal elements found 		   =	      339
 No. of zero elements found			   =		0
 No. of elements close to zero			   =		0    0.00%
 Log determinant given				   =  0.00000
 ***** Found more levels of RE in GIN^{-1} than in data
       No. of levels found in data		   =	      284
       Max. row/column no. in GIN^{-1}		   =	      339



 ***** Looking for file with codes "animal.codes"
 Have read					   =	      339 codes from file "animal.codes"
 Max. number of levels for "animal" set to	   =	      339
**************************** Count of "animal" types ****************************
 No. of non-genotyped animals			   =		0
 No. of genotyped animals in total		   =	      339
 Total no. of "animals" 			   =	      339

 No UNgenotyped animals found
    Zero out: 1st level  1  sex 	     1	 EqNo.	      4
    Zero out: 1st level  1  littersize	     2	 EqNo.	      6
    Zero out: 1st level  2  sex 	     3	 EqNo.	     16
    Zero out: 1st level  2  littersize	     4	 EqNo.	     18
 No. of "subjects" in data			   =	      284
 No. of combinations of records 		   =		1
 No. of effect codes/ind. (maxnr)		   =	       10
 Random effect no.	     0
  1   1.70000
  2   1.00000	    12.6000
 Eigenvalues   12.6910	     1.60902
 in %	       88.7481	     11.2519
 Random effect no.	     1
  1   4.90000
  2   1.00000	    6.00000
 Eigenvalues   6.59127	     4.30873
 in %	       60.4704	     39.5296
 Random effect no.	     2
  1   1.50000
  2   1.00000	    3.00000
 Eigenvalues   3.50000	     1.00000
 in %	       77.7778	     22.2222
 nq,neqns,nnginv	   2	     786	1014	       0  xx   83898.0000000000 	   83898  2147483646
 build MME - data part complete 		   =	     5406
 S1STEP: build MME - random effects part	   =	     5406
  end of peds	     5406
 S1STEP: build MME - 1st pass complete
 Total no. of equations in MME			   =	      786
 No. of non-zero off-diagonal elements (triangle)  =	     5406
 S1STEP: sort linked list - 2nd pass complete
 ZHZ successfully allocated		     5406.
 ZHZDDD successfully allocated		   459684.
  end of peds	     5406
 S1STEP: build MME - 3rd pass complete
 No. of zero elements in ZHZ			   =	     4532
 No. of "genotyped" animals			   =	      339
 No. of "dense" equations - genotyped animals	   =	      678
 ... divided into how many sub-blocks		   =		1
 ... non-zero elements (triangle)		   =  3717.00	   1.61482
 Total no. of non-zero coefficients LHS (inc.diag) =  9227.00
 Pre-conditioning scheme selected		   = "imprssor "
 Dense Cholesky factorisation option		   = "dpotrf"
 Dense LHS multiplication option		   = "dsymv "
 Sparse LHS multiplication option		   = "dsymv "
 Maximum no. of iterates			   =	    50000
 Interval (iterates) to reset residuals 	   =	       75
 Convergence criterion: SS deviations		   = 0.100000E-08
 Convergence criterion: SS dev.s/SS sol.s	   = 0.100000E-06
 S1STEP: start preconditioner at -  cpu 	      0 system		 0 wmb		 0    0.141000E-01
 S1STEP: start PCG iterations at -  cpu 	      0 system		 0 wmb		 0
   PCG	  50	 2.78907	0.943023E-04	0.141728E-04	 12397.3      sys-time		     0.0
   PCG	  61	 2.48317	0.502259E-06	0.507197E-09	 12397.4      sys-time		     0.0
 Final SS(solutions)				   =  12397.4
 Final SS(deviations)				   = 0.507197E-09
 Final SS(dev)/SS(sol)				   = 0.409114E-13
 S1STEP: end PCG iterations at - cpu		  0 system	     0
						 0 system	    0 min
 wtime						   = 0.250000E-01 0.416667E-03 0.694444E-05
 since precond					   = 0.115000E-01 0.191667E-03
	 no. of iterates carried out		   =	       61 imprssor
 No. of OMP threads used			   =		8
 Time for setting up preconditioner		   =  0.00000	   0.00000
Example 18/B: Bivariate S1STEP analysis; mouse data from Example 2
   1  animal		       678  zero soln.s       0
   2  litterno			84  zero soln.s       0
 Total time used (secs): CPU =		 0  System =	       0
 Machine used = "didgeridoo"
 "WOMBAT" has finished !  26/05/2025


0.091u 0.010s 0:00.03 333.3%	0+0k 0+312io 0pf+0w

Script done on 2025-05-26 17:25:31+1000
