As one of the first steps in analyses fitting an animal model, WOMBAT checks the pedigree file supplied against the data file and, if applicable, deletes any individuals not linked to the data in any way. The new, reduced pedigree is written to this file. Like the original pedigree file, it contains 3 columns, i.e. codes for animal, sire and dam.
The second ‘pedigree modification’ carried out is ‘pruning’. This is performed for each genetic effect separately (provided they are assumed to be uncorrelated). The corresponding pedigrees are written to these files, with pertaining to the order in which these effects are specified in the model part of the parameter file. Each has 7 columns: columns 1 to give the animal, sire and dam recoded in running order, columns 4 to 6 give the corresponding original identities, and column 7 contains the inbreeding coefficient of the individual.
This file collects ‘time stamps’ for various stages of a run, together explanatory messages for programmed stops. The content largely duplicates what is written to the screen. However, the file is closed after any message written – in contrast to a capture of the screen output which, under Linux, may be incomplete. It is intended for those running a multitude of analyses and wanting to trace hat went on. N.B. This file is appended too, i.e. will collect information for multiple runs in the current directory if not deleted between runs.