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Command used: wombat w_hdiag2.par
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wombat w_hdiag2.par
Script started on 2025-05-26 17:31:04+1000
 WOMBAT 26-05-2025 Maximum no. of threads to be used set to	      8

 Parameter file opened : "w_hdiag2.par"
**RUNOP --hinv -v**
**COM Example20/A5: calculate diagonals of H ONLY**
**PED ../InputFiles/peds.dat**
  Pedigree file : "../InputFiles/peds.dat"
**MRK ../InputFiles/MarkerCounts.dat**
  Marker counts file : "../InputFiles/MarkerCounts.dat"
**SPECIAL**
**HINVERSE SNP 3000**
  HINV: nsnp, msnp	   3000        3000
 HACK_NUMBER NSNPS
**HINVERSE OUT GIN animal**
  HINV: how_houtput GIN
 animal.gin
**HINVERSE DIAGH ONLY**
**END**

 End of parameter file reached :   9 lines read
 Colleau's method specified for calculation of A22 - but not needed
 ***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/peds.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
 ... TIER's algorithm
 Covariance structure				   =	NRM
 No. of inbred animals				   =	       73
 Average inbreeding coefficient 		   = 0.269792	  (in %)
 ... amongst inbred animals			   =  2.77183	  (in %)

 NRM Inverse no. :	     1	 "X"
 No. of elements =	  2545	 log determinant =  -417.061508887861
 HDIAG: No. of animals in total 		   =	      750
	No. of unrelated + ungenotyped animals	   =	       15
	No. of ungenotyped relatives		   =	      365
	No. genotyped animals			   =	      370
 end count_relatives	      15	 735
 End: centering M2			       sys-time 	    0.4 	    0.4
 No. of non-genotyped relatives of genotypes	   =	      365
 No. of genotyped animals + their relatives	   =	      735
 Total no. of NNZ in A^{-1} read		   =	     2545
 No. of NNZ in submatrix A^11 - reduced 	   =	      837
 No. of NNZ in submatrix A^12 - reduced 	   =	      907
 No. of non-zero elements in A^{11}		   =	      837	   365
 No. of elements in A^{12}			   =	      907	   365
 No. of non-zero elements in A^{21}		   =	      907	   370
 No. of non-zero elements in A^{22}		   =	      786	   370
 Output file with diagonal elements of H	   = "animal.hdiags"
 Elements for non-genotyped ancestors calculated   = ALL
 Method 3 of Legarra & Aguilar: how_mmatrix	   = INDIR
 Total time used (secs): CPU =		 1  System =	       0
 Machine used = "didgeridoo"
 "WOMBAT" has finished !  26/05/2025


1.188u 0.127s 0:00.53 245.2%	0+0k 0+264io 0pf+0w

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