======================================================
Command used: wombat w_hinv_MFggrp.par
======================================================

wombat w_hinv_MFggrp.par
Script started on 2025-05-26 17:32:09+1000
 WOMBAT 26-05-2025 Maximum no. of threads to be used set to	      8

 Parameter file opened : "w_hinv_MFggrp.par"
**RUNOP  -v --hinv**
**PED ../pedMFggrp.dat**
  Pedigree file : "../pedMFggrp.dat"
**MRK ../MarkerCounts.dat**
  Marker counts file : "../MarkerCounts.dat"
**SPECIAL**
**HINVERSE SNP 400**
  HINV: nsnp, msnp	    400 	400
 HACK_NUMBER NSNPS
**HINVERSE out GIN animal**
  HINV: how_houtput GIN
 animal.gin
**HINVERSE lambda 1.0**
  HINV: lambda	  1.00000000000000
**HINVERSE epsilon 0.1d0**
  HINV: epsilon   0.100000000000000
**HINVERSE center half**
  HINV: how_center HALF  5.000000000000000E-002
**GENGROUPS gggrps 6 10000**
 HACK_NUMBER GGRPS
 SPECIAL: Fit "explicit" genetic groups
 No. of groups given	       :	   6
 Scale factor for proportions  :   10000.0000000000
**HINVERSE  metafounder -6 emalg SCALED**
  HINV: mf_gamma1   -6.00000000000000
 HACK_NUMBER METAF
 trying to estimate matrix GAMMA
  HINV: set up A-gamma inverse scaled  T emalg	       200
**END**

 End of parameter file reached :  12 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
 Expect to read genetic group proportions from pedigree file
 ->  column no.s	   5  to	  10
    (need "animal type" variable even if not required otherwise)
 Pedigree file					   = ../pedMFggrp.dat
 Total no. of animal IDs found			   =	     5006
 ***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			   =	     5000
 no. of NRM matrices		1	    1
**************************** Count of "animal" types ****************************
 No. of non-genotyped animals			   =	     3522
 No. of genotyped animals in total		   =	     1478
 Total no. of "animals" 			   =	     5000

 Begin: read M2 from ../MarkerCounts.dat       sys-time 	    0.1 	    0.1
 tvec4	       400
 chevck marks	      400	  400
 No. of rows in ../MarkerCounts.dat read	   =	     1478
 No. of marker allele counts per row read	   =	      400
 End: read M2 from .dat 		       sys-time 	    0.2 	    0.2

 Inbreeding coefficients for random effect	   =		1 computed
 ... MEUWISSEN & LIU algorithm
 Covariance structure				   =	NRM
 No. of inbred animals				   =	     2627
 Average inbreeding coefficient 		   =  1.06432	  (in %)
 ... amongst inbred animals			   =  2.02330	  (in %)

 NRM Inverse no. :	     1	 "X"
 No. of elements =	 18417	 log determinant =  -3165.11004461527
 A22: No. genotyped animals + ancestors 	   =	     2871
 End: calculating A22 (Colleau) 	       sys-time 	    0.3 	    0.3
      MF emalg		 1 change  0.223709563087219
      MF emalg		 2 change  2.106644244007731E-003
      MF emalg		 3 change  1.176232277122412E-004
      MF emalg		 4 change  2.485758138217104E-005
      MF emalg		 5 change  8.324826387101614E-006
      MF emalg		 6 change  3.589574777509295E-006
      MF emalg		 7 change  1.813489988682583E-006
      MF emalg		 8 change  1.021077060080672E-006
      MF emalg		 9 change  6.220661118261058E-007
      MF emalg		10 change  4.023778435049283E-007
 ************* Estimating degree(s) of self-relationship for metafounders ************
 No. of metafounders				   =		6
 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				   =	      400	   400
 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  0.5867  0.5672  0.5610  0.5819  0.5729  0.5727
    2  0.5672  0.5655  0.5526  0.5726  0.5652  0.5645
    3  0.5610  0.5526  0.5527  0.5663  0.5577  0.5579
    4  0.5819  0.5726  0.5663  0.5925  0.5782  0.5792
    5  0.5729  0.5652  0.5577  0.5782  0.5777  0.5711
    6  0.5727  0.5645  0.5579  0.5792  0.5711  0.5740

    1  1.0000  0.9847  0.9851  0.9869  0.9840  0.9869
    2  0.9847  1.0000  0.9884  0.9892  0.9888  0.9908
    3  0.9851  0.9884  1.0000  0.9896  0.9871  0.9904
    4  0.9869  0.9892  0.9896  1.0000  0.9882  0.9932
    5  0.9840  0.9888  0.9871  0.9882  1.0000  0.9918
    6  0.9869  0.9908  0.9904  0.9932  0.9918  1.0000

 ***Time: begin idvec			      1 	  0 Used since last	    1.4 	0.3
 ***Time: end idvec			      1 	  0 Used since last	    0.0 	0.0
 Expect to read genetic group proportions from pedigree file
 ->  column no.s	   5  to	  10
    (need "animal type" variable even if not required otherwise)
 Pedigree file					   = ../pedMFggrp.dat
 Total no. of animal IDs found			   =	     5006
 no. of NRM matrices		1	    1
**************************** Count of "animal" types ****************************
 No. of non-genotyped animals			   =	     3528
 No. of genotyped animals in total		   =	     1478
 Total no. of "animals" 			   =	     5006

 Full GRM inverse specied but no. of SNPs less than no. of genotypes
 No. of genotyped individuals found =	     1478
 No. of markers used		    =	      400
 Using WOODBURY form of inverse might be advantageous??
 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
 MF	      4 	  4	      0 	  0
 MF	      5 	  5	      0 	  0
 MF	      6 	  6	      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				   =	     5000
 Average inbreeding coefficient 		   =  29.3026	  (in %)
 ... amongst inbred animals			   =  29.3026	  (in %)

 NRM Inverse no. :	     1	 "X"
 No. of elements =	 18938	 log determinant =  0.000000000000000E+000
 A22: No. genotyped animals + ancestors 	   =	     2877
 End: calculating A22 (Colleau) 	       sys-time 	    0.5 	    0.5
 End: centering M2			       sys-time 	    0.5 	    0.5
 End: calculating GRM			       sys-time 	    0.6 	    0.6
 end calc g22 T
 F
 End: inverting g22			       sys-time 	    0.6 	    0.6
 End: inverting a22			       sys-time 	    0.6 	    0.6
 Start writing out "animal.gin"
 Successfully allocated arrays for in-core NRM
 NRM Inverse no. :	     1	 "X"
 No. of elements =	 18938	 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   =	   1109379.0
	 0.00000		  alpha 	  0.00000
 Total time used (secs): CPU =		 6  System =	       3
 Machine used = "didgeridoo"
 "WOMBAT" has finished !  26/05/2025


5.396u 1.493s 0:03.14 219.1%	0+0k 0+110096io 0pf+0w

Script done on 2025-05-26 17:32:12+1000
======================================================
Command used: wombat blup_MFggrp.par
======================================================

wombat blup_MFggrp.par
Script started on 2025-05-26 17:32:12+1000
 WOMBAT 26-05-2025 Maximum no. of threads to be used set to	      8

 HACK_NUMBER GGRPS
 SPECIAL: Fit "explicit" genetic groups
 No. of groups given	       :	   6
 Scale factor for proportions  :   10000.0000000000
 Random effect in model        : "gggrps"
 "Animal" effect corresponding to genetic groups
 set to "animal" GIN
 Read genetic group proportions from .codes file!
	  50	      50 6  0.718231
 File						   = "animal.gin"
 No. of records 				   =	  1109379
 Denseness of matrix				   =  8.85200	 %
 No. of diagonal elements found 		   =	     5006
 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		   =	     5000
       Max. row/column no. in GIN^{-1}		   =	     5006



 Have read					   =	     5006 codes from file "animal.codes"
 Max. number of levels for "animal" set to	   =	     5006
 No. of "subjects" in data			   =	     5000
 No. of combinations of records 		   =		1
 No. of effect codes/ind. (maxnr)		   =		3
 adjact ivcol	 27542268    27542268
 Start of "GENMMD": no. of rows 		   =	     5022
 End of "GENMMD": no of subscripts		   =	   419927
 adjact ivcol	 27542268    27542268
 End of "SMBFCT": maxsub			   =	   338604	  5023
		  maxlnz			   =	  1534998
		  nnops 			   = 0.798727E+09 0.100000E+16
 "Super-nodes" :  No. of nodes			   =	     3240
		  Max. size			   =	     1482
   1  animal		      5006  zero soln.s       0
   2  gggrps			 6  zero soln.s       0
 SS residuals	5964.45
 Total time used (secs): CPU =		 7  System =	       5
 Machine used = "didgeridoo"
 "WOMBAT" has finished !  26/05/2025


7.196u 0.319s 0:05.92 126.6%	0+0k 0+24560io 0pf+0w

Script done on 2025-05-26 17:32:18+1000
