======================================================
Command used: wombat w_hinv_phant.par
======================================================

wombat w_hinv_phant.par
Script started on 2025-05-26 17:31:51+1000
 WOMBAT 26-05-2025 Maximum no. of threads to be used set to	      8

 Parameter file opened : "w_hinv_phant.par"
**RUNOP  -v --hinv**
**PED ../pedupg.dat**
  Pedigree file : "../pedupg.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  alpha -9.d0**
  HINV: alpha	-9.00000000000000	 T
**GENGROUPS gggrps 6 -9 phantomA22**
 HACK_NUMBER GGRPS
 SPECIAL: Fit "phantom" parents as genetic groups
 No. of groups given	       :	   6
 Scale factor for proportions  :  -9.00000000000000
**END**

 End of parameter file reached :  11 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
 Expect to read unknown parent group codes from pedigree file
 ->  column no.s	   5  to	   6
    (need "animal type" variable even if not required otherwise)
 Pedigree file					   = ../pedupg.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

 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??
 Begin: read M2 from ../MarkerCounts.dat       sys-time 	    0.0 	    0.0
 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
 Successfully allocated arrays for in-core NRM

 Inbreeding coefficients for random effect	   =		1 computed
 ... TIER's algorithm
 Covariance structure				   =	NRM
 No. of inbred animals				   =	     2627
 Average inbreeding coefficient 		   =  1.06304	  (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
 End: centering M2			       sys-time 	    0.4 	    0.4
 End: calculating GRM			       sys-time 	    0.4 	    0.4
 end calc g22 F
 F
 halpha   1.877289474467664E-002  gbar -8.430946489377720E-018	abar  1.877289474467663E-002
 End: inverting g22			       sys-time 	    0.4 	    0.4
 End: inverting a22			       sys-time 	    0.4 	    0.4
 phantom_grrps: UPG instead of Q-matrix not implmented
QHHQ  1   25.263     -0.10943	   0.14437     -0.39747     -0.29765	 -0.19404
QHHQ  2 -0.10943       45.844	  -0.94105E-02	-1.0539     -0.46481	 -0.30366
QHHQ  3  0.14437     -0.94105E-02   41.985     -0.35524     -0.61043	 -0.75446
QHHQ  4 -0.39747      -1.0539	  -0.35524	 57.883     -0.76914	  -1.3613
QHHQ  5 -0.29765     -0.46481	  -0.61043     -0.76914       50.450	 -0.43502
QHHQ  6 -0.19404     -0.30366	  -0.75446	-1.3613     -0.43502	   70.561
 Start writing out "animal.gin"
 H^{-1} : No. of non-zero elements in A^11, A^21   =	   1108858.0
Aqhq  5001    25.263306    -0.109431	 0.144374    -0.397475	  -0.297648    -0.194036
Aqhq  5002    -0.109431    45.843512	-0.009410    -1.053874	  -0.464808    -0.303661
Aqhq  5003     0.144374    -0.009410	41.985183    -0.355243	  -0.610428    -0.754465
Aqhq  5004    -0.397475    -1.053874	-0.355243    57.882681	  -0.769140    -1.361317
Aqhq  5005    -0.297648    -0.464808	-0.610428    -0.769140	  50.450191    -0.435021
Aqhq  5006    -0.194036    -0.303661	-0.754465    -1.361317	  -0.435021    70.561361
	0.187729E-01		  alpha 	 0.187729E-01
 Total time used (secs): CPU =		 4  System =	       2
 Machine used = "didgeridoo"
 "WOMBAT" has finished !  26/05/2025


3.544u 1.451s 0:02.98 167.4%	0+0k 0+107496io 0pf+0w

Script done on 2025-05-26 17:31:54+1000
======================================================
Command used: wombat blup_phant.par
======================================================

wombat blup_phant.par
Script started on 2025-05-26 17:31:54+1000
 WOMBAT 26-05-2025 Maximum no. of threads to be used set to	      8

 HACK_NUMBER GGRPS
 "phantom genetic groups only tested for --s1step/blup runs
 SPECIAL: Fit "phantom" parents as genetic groups
 No. of groups given	       :	   6
 Scale factor for proportions  :  -9.00000000000000
 Random effect in model        : "gggrps"
 Corresponding "animal" effect : "animal"
	  50	      50 0   1.00000
 File						   = "animal.gin"
 No. of records 				   =	  1117098
 Denseness of matrix				   =  8.91359	 %
 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"
 No. of "phantom groups"			   =		6
 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	 27704718    27704718
 Start of "GENMMD": no. of rows 		   =	     5016
 End of "GENMMD": no of subscripts		   =	   417085
 adjact ivcol	 27704718    27704718
 End of "SMBFCT": maxsub			   =	   334562	  5017
		  maxlnz			   =	  1512719
		  nnops 			   = 0.793551E+09 0.100000E+16
 "Super-nodes" :  No. of nodes			   =	     3239
		  Max. size			   =	     1480
   1  animal		      5006  zero soln.s       0
   2  gggrps			 0  zero soln.s       0
 SS residuals	6086.50
 Total time used (secs): CPU =		 6  System =	       5
 Machine used = "didgeridoo"
 "WOMBAT" has finished !  26/05/2025


6.514u 0.367s 0:05.62 122.2%	0+0k 0+22912io 0pf+0w

Script done on 2025-05-26 17:32:00+1000
