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Command used: wombat w_hinvmeta3.par
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wombat w_hinvmeta3.par
Script started on 2025-05-26 17:31:12+1000
 WOMBAT 26-05-2025 Maximum no. of threads to be used set to	      8

 Parameter file opened : "w_hinvmeta3.par"
**RUNOP --hinv -v**
**COM Ecxample20/L: calculate H^{-1} with A^{-Gamma} for 3 MF; estimate Gamma**
**PED ../InputFiles/pedsMF3.dat**
  Pedigree file : "../InputFiles/pedsMF3.dat"
**MRK ../InputFiles/MarkerCounts.dat**
  Marker counts file : "../InputFiles/MarkerCounts.dat"
**SPECIAL**
**HINVERSE SNP 3000**
  HINV: nsnp, msnp	   3000        3000
 HACK_NUMBER NSNPS
**HINVERSE META -3 SCALE EMALG**
  HINV: mf_gamma1   -3.00000000000000
 HACK_NUMBER METAF
 trying to estimate matrix GAMMA
  HINV: set up A-gamma inverse scaled  T emalg	       200
**HINVERSE CENTER half**
  HINV: how_center HALF  5.000000000000000E-002
**END**

 End of parameter file reached :   9 lines read
 Colleau's method specified for calculation of A22 - but not needed
 Working out ancestry proportions for metafounders
 ***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					   = ../InputFiles/pedsMF3.dat
 Total no. of animal IDs found			   =	      753
 ***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					   = tmpped.dat
 Total no. of animal IDs found			   =	      750
 no. of NRM matrices		1	    1
**************************** Count of "animal" types ****************************
 No. of non-genotyped animals			   =	      380
 No. of genotyped animals in total		   =	      370
 Total no. of "animals" 			   =	      750

 Begin: read M2 from ../InputFiles/MarkerCount sys-time 	    0.0 	    0.0
 tvec4	      3000
 chevck marks	     3000	 3000
 No. of rows in ../InputFiles/MarkerCounts.dat read=	      370
 No. of marker allele counts per row read	   =	     3000
 End: read M2 from .dat 		       sys-time 	    0.3 	    0.3

 Inbreeding coefficients for random effect	   =		1 computed
 ... MEUWISSEN & LIU algorithm
 Covariance structure				   =	NRM
 No. of inbred animals				   =	       73
 Average inbreeding coefficient 		   = 0.270875	  (in %)
 ... amongst inbred animals			   =  2.77183	  (in %)

 NRM Inverse no. :	     1	 "X"
 No. of elements =	  2545	 log determinant =  -417.061508887861
 A22: No. genotyped animals + ancestors 	   =	      624
 End: calculating A22 (Colleau) 	       sys-time 	    0.3 	    0.3
      MF emalg		 1 change  0.362532762488467
      MF emalg		 2 change  2.964508878202129E-003
      MF emalg		 3 change  2.341811256093051E-004
      MF emalg		 4 change  5.575870340473540E-005
      MF emalg		 5 change  1.990022506456980E-005
      MF emalg		 6 change  8.837560852550027E-006
      MF emalg		 7 change  4.496862660912718E-006
      MF emalg		 8 change  2.512664935284575E-006
      MF emalg		 9 change  1.503628640741564E-006
      MF emalg		10 change  9.483711368300139E-007
      MF emalg		11 change  6.236673901940901E-007
 ************* Estimating degree(s) of self-relationship for metafounders ************
 No. of metafounders				   =		3
 Method to deal with missing genotype info.	   = SETUNITY
 Diagonals of Gamma for "missing" MF set to	   = 0.500000E-01
 Minimum allele frequency allowed		   =  0.00000
 No. of markers used				   =	     3000	  3000
 Threshold to disregard MF with Diag( Q'A22^{-1}Q) = 0.100000E-07
 Method to estimate "Gamma"			   = emalg
 Max. no. of iterates allowed			   =	      200
    1  0.2776  0.2376  0.2512
    2  0.2376  0.2767  0.2265
    3  0.2512  0.2265  0.2545

    1  1.0000  0.8575  0.9449
    2  0.8575  1.0000  0.8535
    3  0.9449  0.8535  1.0000

 ***Time: begin idvec			      0 	  0 Used since last	    0.9 	0.4
 ***Time: end idvec			      0 	  0 Used since last	    0.0 	0.0
 Pedigree file					   = ../InputFiles/pedsMF3.dat
 Total no. of animal IDs found			   =	      753
 no. of NRM matrices		1	    1
**************************** Count of "animal" types ****************************
 No. of non-genotyped animals			   =	      383
 No. of genotyped animals in total		   =	      370
 Total no. of "animals" 			   =	      753

 Fitting meta-founder(s) - forcing re-build of NRM Inverse
 MF	      1 	  1	      0 	  0
 MF	      2 	  2	      0 	  0
 MF	      3 	  3	      0 	  0
 start get_mfgamma22
 Matrix Gamma for metafounders has been estimated

 Inbreeding coefficients for random effect	   =		1 computed
 ... MEUWISSEN & LIU algorithm
 Covariance structure				   =	NRM
 No. of inbred animals				   =	      750
 Average inbreeding coefficient 		   =  12.6713	  (in %)
 ... amongst inbred animals			   =  12.6713	  (in %)

 NRM Inverse no. :	     1	 "X"
 No. of elements =	  2810	 log determinant =  0.000000000000000E+000
 A22: No. genotyped animals + ancestors 	   =	      627
 End: calculating A22 (Colleau) 	       sys-time 	    0.4 	    0.4
 End: centering M2			       sys-time 	    0.4 	    0.4
 End: calculating GRM			       sys-time 	    0.4 	    0.4
 end calc g22 T
 F
 End: inverting g22			       sys-time 	    0.4 	    0.4
 End: inverting a22			       sys-time 	    0.4 	    0.4
 Start writing out "Hinverse.gin"
 Successfully allocated arrays for in-core NRM
 NRM Inverse no. :	     1	 "X"
 No. of elements =	  2810	 log determinant =  0.000000000000000E+000
 Succesfully read from file for in-core storage
 H^{-1} : No. of non-zero elements in A^11, A^21   =	   70659.000
	 0.00000		  alpha 	  0.00000
 Total time used (secs): CPU =		 2  System =	       0
 Machine used = "didgeridoo"
 "WOMBAT" has finished !  26/05/2025


2.239u 0.151s 0:00.57 417.5%	0+0k 0+7784io 0pf+0w

Script done on 2025-05-26 17:31:13+1000
