======================================================
Command used: wombat hinv_delta.par
======================================================

wombat hinv_delta.par
Script started on 2025-05-26 17:31:15+1000
 WOMBAT 26-05-2025 Maximum no. of threads to be used set to	      8

 Parameter file opened : "hinv_delta.par"
**RUNOP  --hinv -v**
**COM Example21/B: step 1. Generate "add-on" to A^{-1} to form H^{-1}**
**PED ../pedigree.dat**
  Pedigree file : "../pedigree.dat"
**MRK ../MarkerCounts.dat**
  Marker counts file : "../MarkerCounts.dat"
**SPECIAL**
**HINVERSE SNP 1000**
  HINV: nsnp, msnp	   1000        1000
 HACK_NUMBER NSNPS
**HINVERSE lambda 1.0**
  HINV: lambda	  1.00000000000000
**HINVERSE epsilon  0.05d0**
  HINV: epsilon   5.000000000000000E-002
**HINVERSE out delta**
  HINV: how_houtput DELTA
**END**

 End of parameter file reached :  10 lines read
 Colleau's method specified for calculation of A22 - but not needed
 "In core" storage for NRM Inverse switched on
 ***Time: begin idvec			      0 	  0 Used since last	    0.0 	0.0
 ***Time: end idvec			      0 	  0 Used since last	    0.0 	0.0
 Pedigree file					   = ../pedigree.dat
 Total no. of animal IDs found			   =	      600
 no. of NRM matrices		1	    1
**************************** Count of "animal" types ****************************
 No. of non-genotyped animals			   =	      313
 No. of genotyped animals in total		   =	      287
 Total no. of "animals" 			   =	      600

 Begin: read M2 from ../MarkerCounts.dat       sys-time 	    0.0 	    0.0
 tvec4	      1000
 chevck marks	     1000	 1000
 No. of rows in ../MarkerCounts.dat read	   =	      287
 No. of marker allele counts per row read	   =	     1000
 End: read M2 from .dat 		       sys-time 	    0.1 	    0.1
 Successfully allocated arrays for in-core NRM

 Inbreeding coefficients for random effect	   =		1 computed
 ... TIER's algorithm
 Covariance structure				   =	NRM
 No. of inbred animals				   =	       24
 Average inbreeding coefficient 		   = 0.500000	  (in %)
 ... amongst inbred animals			   =  12.5000	  (in %)

 NRM Inverse no. :	     1	 "X"
 No. of elements =	  1780	 log determinant =  -277.258872223979
 A22: No. genotyped animals + ancestors 	   =	      368
 End: calculating A22 (Colleau) 	       sys-time 	    0.2 	    0.2
 End: centering M2			       sys-time 	    0.2 	    0.2
 End: calculating GRM			       sys-time 	    0.2 	    0.2
 end calc g22 F
 F
 End: inverting g22			       sys-time 	    0.2 	    0.2
 End: inverting a22			       sys-time 	    0.2 	    0.2
 Start writing out "Hinverse-Delta.BIN"     287
	 0.00000		  alpha 	  0.00000
 Total time used (secs): CPU =		 1  System =	       0
 Machine used = "didgeridoo"
 "WOMBAT" has finished !  26/05/2025


0.948u 0.166s 0:00.31 354.8%	0+0k 0+2008io 0pf+0w

Script done on 2025-05-26 17:31:15+1000
======================================================
Command used: wombat s2step.par
======================================================

wombat s2step.par
Script started on 2025-05-26 17:31:15+1000
 WOMBAT 26-05-2025 Maximum no. of threads to be used set to	      8

	   1 xone
	   2 xtwo
  skipping check for sorting of data
 Pedigree file					   = ../pedigree.dat
 Total no. of animal IDs found			   =	      600
 *** "Iteration on data" module for single step analyses ***
 This run requires "Hinverse-Delta.BIN" supplying G^{-1} - A22^{-1}
**************************** Count of "animal" types ****************************
 No. of non-genotyped animals			   =	      313
 No. of genotyped animals in total		   =	      287
 Total no. of "animals" 			   =	      600

	 600	      40 F F F
 Successfully allocated arrays for in-core DATA
 alloc cor nr	      600	   40 T T T
 No. of "subjects" in data			   =	      600
 No. of combinations of records 		   =		1
 No. of effect codes/ind. (maxnr)		   =		4
 Random effect no.	     0
  1   1.19670
  2   1.16150	    12.5249
 Eigenvalues   12.6428	     1.07884
 in %	       92.1377	     7.86232
 Random effect no.	     1
  1   1.19670
  2  0.666500	    3.13120
 Eigenvalues   3.33860	    0.989303
 in %	       77.1413	     22.8587
 No. of "Delta" coefficients read		   =	    41328 from "Hinverse-Delta.BIN"
 end data
 S2STEP: start preconditioner	 -  cpu 	  0 system	     0 wmb	     0	  0.142400
 S2STEP: start PCG iterations at -  cpu 	  0  system	      0  wmb	       0
   PCG	  50	 1.25662	0.891561E-03	0.418650E-02	 8316.81      sys-time		     0.1
   PCG	 100	 1.25634	0.118917E-05	0.744702E-08	 8312.07      sys-time		     0.2
   PCG	 108	 1.24691	0.368170E-06	0.724663E-09	 8312.07      sys-time		     0.2
 Final SS(solutions)				   =  8312.07
 Final SS(deviations)				   = 0.724663E-09
 Final SS(dev)/SS(sol)				   = 0.871820E-13
 S2STEP: end PCG iterations at - cpu		  0 system	     0
						 0 system	    0 min
 wtime						   = 0.156000	  0.260000E-02 0.433333E-04
 wtime since precond				   = 0.130000E-01 0.216667E-03
	 no. of iterates carried out		   =	      108  diagonals	0.10000E-06    0.10000E-08
	 no. of threads used			   =		8
Example21/B: Step 2 - SS-GBLUP run using iteration on data
   1  aanimal		      1200  zero soln.s       0
 ***  Single-step BLUP using iteration on data	***
 Pre-conditioning scheme selected		   = "diagonals"
 Diagonal blocks for genetic groups in core	   =  T
 Store elements of H^22-A^22 in core		   =  T
 Store recoded data in core			   =  T
 Dense Cholesky factorisation option		   = "dpotrf"
 Dense LHS multiplication option		   = "dsymv "
 Option for processing elements of NRM inverse	   = "colloo"
 Option for evaluating data parts		   = "calcul"
 Maximum no. of iterates			   =	    50000
 Interval (iterates) to print information	   =	       50
 Interval (iterates) to reset residuals 	   =	      100
 Interval (iterates) to check convergence	   =	       10
 Convergence criterion: SS deviations		   = 0.100000E-08
 Convergence criterion: SS dev.s/SS sol.s	   = 0.100000E-06
 Number of traits				   =		2
 ... principal components			   =  F
 Number of equations in MME			   =	     1814
 Number of non-genotyped animals		   =	      313
 Number of genotyped animals			   =	      287
 Total time used (secs): CPU =		 0  System =	       0
 Machine used = "didgeridoo"
 "WOMBAT" has finished !  26/05/2025


0.376u 0.086s 0:00.16 281.2%	0+0k 0+408io 0pf+0w

Script done on 2025-05-26 17:31:15+1000
