======================================================
Command used: wombat snappy3.par
======================================================

wombat snappy3.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 : "snappy3.par"
**RUNOP  --snap -v**
**ANAL UNI**
  Analysis type = 1  "UNI"
  No. of traits =  1
**PEDS ../SimPed.dat**
  Pedigree file : "../SimPed.dat"
**DATA ../SimData2.dat**
  Data file : "../SimData2.dat"
**traitno  2**
traitno  2
 Warning: Column name starting with "TR" found
	  Treated as column name rather than trait specifier
  Data - column :	 1  "traitno"	      2
**animal   0**
  Data - column :	 2  "animal"	     0
**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
**xxx**
  Data - column :	 9  "xxx"	 -1
**end**
**MODEL**
**FIX  kfix**
**FIX  mfix**
**COV  snp(1)**
**COV  znp(1)**
**COV  age(2)**
**RAN animal  nrm**
**trait  xxx**
  Trait no.  1	"xxx"  Missing value  -123456789
**END MOD**
**VAR animal 1**
**30**
**VAR residual 1**
**90**
**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 :  33 lines read
 Data file appers to be sorted correctly
 No. of records in total			   =	       16
 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 =		   =		1	   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.	      8
 No. of "subjects" in data			   =	       16
 No. of combinations of records 		   =		1
 No. of effect codes/ind. (maxnr)		   =		3
 Parameters to be estimated & their starting values
    1  COVS Z 1 1	    90.000000	  F
    2  COVS A 1 1	    30.000000	  F
 LSQ: END data - nrczhz =	   36
 Coefficient matrix fixed effects - rank =     9  no. of rows =    10
    Zero Out	       1  Row/Columnn No.	    8
 END "lsqfixed"
 No. of equations in full rank submatrix =	    35
 nq,neqns,nnginv	   1	      36	  66  xx   2508.00000000000		2508  2147483646
 QTLSKIP	   1 eq no	     1
 QTLSKIP	   2 eq no	     2
 No. of equations in full rank submatrix =	    33
 adjact ivcol	    22572	22572
 Elements in MMM - after data		       72
 Elements in MMM - after RE    1	      112
 Start of "GENMMD": no. of rows 		   =	       33
 End of "GENMMD": no of subscripts		   =	      116
 No. of equations in full rank submatrix =	    35
 adjact ivcol	    22572	22572
 Elements in MMM - after data		      112
 Elements in MMM - after RE    1	      152
 adjact ivcol	    22572	22572
 Elements in MMM - after RHS		      175
 End of "SMBFCT": maxsub			   =	      166	    36
		  maxlnz			   =	      211
		  nnops 			   =  1076.00	  0.100000E+16
 END "eqnorders"
 MAXLNZ 	211
node size =	    1 n =	  19
node size =	    3 n =	   2
node size =	   11 n =	   1
 "Super-nodes" :  No. of nodes			   =	       22
		  Max. size			   =	       11
 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)
     44.8303	     14.0814	     3.18366	   SNPeffect1-1
    -7.56106	     5.74596	    -1.31589	   SNPeffect1-2
     28.6272	     9.00189	     3.18013	   SNPeffect2-1
    -5.57936	     5.32652	    -1.04747	   SNPeffect2-2
     29.8776	     8.86335	     3.37092	   SNPeffect3-1
    -3.67384	     5.34465	   -0.687386	   SNPeffect3-2
     25.4611	     8.13868	     3.12840	   SNPeffect4-1
     3.92823	     5.02431	    0.781846	   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


0.215u 0.184s 0:00.30 130.0%	0+0k 0+120io 0pf+0w

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