======================================================
Command used: wombat snappy4.par
======================================================

wombat snappy4.par
Script started on 2025-05-26 17:15:58+1000
 WOMBAT 26-05-2025 Maximum no. of threads to be used set to	      8

 Parameter file opened : "snappy4.par"
**RUNOP  --snap -v**
**COM Example14/D: 2 traits, 2 SNPs at a time**
**ANAL MUV 2**
  Analysis type = 2  "MUV 2"
  No. of traits =  2
**PEDS ../SimPed.dat**
  Pedigree file : "../SimPed.dat"
**DATA ../SimDataBiv2.dat  GRP**
  Data file : "../SimDataBiv2.dat"
**TRNOS  1  2**
**traitno  2**
  Data - column :      1  "traitno"	    2
**animal   0**
  Data - column :      2  "animal"	  -1
**kfix	   10**
  Data - column :      3  "kfix"	10
**mfix	   33**
  Data - column :      4  "mfix"	33
**lint	  999**
  Data - column :      5  "lint"       999
**snp**
  Data - column :      6  "snp"        -1
**znp**
  Data - column :      7  "znp"        -1
**age**
  Data - column :      8  "age"        -1
**NAMES  xxx  yyy**
	   1 xxx
	   2 yyy
**end**
**MODEL**
**FIX  kfix**
**FIX  mfix**
**COV  snp(1)**
**COV  znp(1)**
**COV  age(2)**
**RAN animal  nrm**
**trait  xxx 1**
  Trait no.  1	"xxx"  Missing value  -123456789
**trait  yyy 2**
  Trait no.  2	"yyy"  Missing value  -123456789
**END MOD**
**VAR animal 2**
**30  -30  60**
**VAR residual 2**
**90  30   180**
**SPECIAL**
**COVZER snp(1) FIT**
 Covariable:"snp(1)" Treat values of 0 as: FIT
**COVZER znp(1) FIT**
 Covariable:"znp(1)" Treat values of 0 as: FIT
**SNPEFF snp(1)**
**SNPEFF znp(1)**
**END**

 End of parameter file reached :  36 lines read
 Data file appers to be sorted correctly
 No. of records in total			   =	       32
 No. of animal IDs in data			   =	       16
 Routine "REDUCEPEDS" to eliminate animals not connected to the data
 -> this may not account properly for genotyped animals & their ancestors
    do not use this routine if you have such information - perform equivalent
    calculations yourself prior to running WOMBAT & use run option --norped
"../SimPed.dat": skipping first  2 lines
 No. of animal IDs in data			   =	       16
 ***Time: begin idvec			      0 	  0 Used since last	    0.2 	0.2
 ***Time: end idvec			      0 	  0 Used since last	    0.0 	0.0
 Pedigree file					   = ../SimPed.dat
 Total no. of animal IDs found			   =	       26
 no. of NRM matrices		1	    1
 Pruned pedigree for random effect no.		 1
 Original no. of animals =	    26
 New no. of animals	 =	    26
 No. of "subjects" in data			   =	       16
 Maximum no. of records/individual =		   =		2	   399

 Inbreeding coefficients for random effect	   =		1 computed
 ... TIER's algorithm
 Covariance structure				   =	NRM
 No. of inbred animals				   =		0
 Average inbreeding coefficient 		   =  0.00000	  (in %)

 File "PrunedPedFile1.dat" written
 NRM Inverse no. :	     1	 "animal"
 No. of elements =	    66	 log determinant =  -11.0903548889591
    Zero out: 1st level  1  mfix	     1	 EqNo.	     12
    Zero out: 1st level  2  mfix	     2	 EqNo.	     18
 No. of "subjects" in data			   =	       16
 No. of combinations of records 		   =		1
 No. of effect codes/ind. (maxnr)		   =		6
 Parameters to be estimated & their starting values
    1  COVS Z 1 1	    90.000000	  F
    2  COVS Z 1 2	    30.000000	  F
    3  COVS Z 2 2	    180.00000	  F
    4  COVS A 1 1	    30.000000	  F
    5  COVS A 1 2	   -30.000000	  F
    6  COVS A 2 2	    60.000000	  F
 LSQ: END data - nrczhz =	   74
 Coefficient matrix fixed effects - rank =    18  no. of rows =    20
    Zero Out	       1  Row/Columnn No.	   12
    Zero Out	       2  Row/Columnn No.	   18
 END "lsqfixed"
 No. of equations in full rank submatrix =	    70
 nq,neqns,nnginv	   2	      72	  66  xx   7524.00000000000		7524  2147483646
 QTLSKIP	   1 eq no	     1
 QTLSKIP	   2 eq no	     2
 QTLSKIP	   3 eq no	     3
 QTLSKIP	   4 eq no	     4
 No. of equations in full rank submatrix =	    66
 adjact ivcol	    67716	67716
 Elements in MMM - after data		      335
 Elements in MMM - after RE    1	      505
 Start of "GENMMD": no. of rows 		   =	       66
 End of "GENMMD": no of subscripts		   =	      260
 No. of equations in full rank submatrix =	    70
 adjact ivcol	    67716	67716
 Elements in MMM - after data		      501
 Elements in MMM - after RE    1	      671
 adjact ivcol	    67716	67716
 Elements in MMM - after RHS		      717
 End of "SMBFCT": maxsub			   =	      326	    71
		  maxlnz			   =	      873
		  nnops 			   =  7899.00	  0.100000E+16
 END "eqnorders"
 MAXLNZ 	873
node size =	    2 n =	  17
node size =	    4 n =	   2
node size =	    8 n =	   1
node size =	   21 n =	   1
 "Super-nodes" :  No. of nodes			   =	       21
		  Max. size			   =	       21
 Start: factorisation of C  sys-time		   0.3
 End: factorisation of C  sys-time		 0.3
 Starting loop over SNPs ...
 File "SNPCounts.dat" found & opened
 Reading SNP allele counts with format: (16i1)
     10.9879	    -33.9018	     6.97806	     9.86847	     1.57464	    -3.43537	    SNPeffect1-1
    -24.7425	    -11.7771	     4.64376	     6.56728	    -5.32812	    -1.79330	    SNPeffect1-2
     16.4291	    -30.0695	     6.92952	     9.79983	     2.37088	    -3.06837	    SNPeffect2-1
    -28.3696	    -13.2575	     4.65513	     6.58335	    -6.09426	    -2.01379	    SNPeffect2-2
     18.2003	    -30.0500	     7.23522	     10.2322	     2.51552	    -2.93682	    SNPeffect3-1
    -29.6283	    -13.0857	     5.23846	     7.40830	    -5.65592	    -1.76636	    SNPeffect3-2
     12.3774	    -38.9281	     7.17873	     10.1523	     1.72418	    -3.83443	    SNPeffect4-1
    -19.2873	    -9.06843	     3.98611	     5.63722	    -4.83862	    -1.60867	    SNPeffect4-2

 "Snappy":	     4 cases for	    2  SNPs
 Output file for estimates: "SNPSolutions.dat"
 Total time used (secs): CPU =		 0  System =	       0
 Machine used = "didgeridoo"
 "WOMBAT" has finished !  26/05/2025


0.260u 0.186s 0:00.33 133.3%	0+0k 0+136io 0pf+0w

Script done on 2025-05-26 17:15:58+1000
