13. Diagnostic messages

Most of the ASPEX diagnostics relate to errors in the marker data and/or parameter files, and all the programs generate similar messages:

? inconsistent data in family 'x': marker(s) 'x', 'x'...

The marker data at the specified position(s) contains a Mendelian inconsistency, possibly due to a typing error, nonpaternity, or a new mutation. The marker data at these positions will be left out of the IBD calculations for this family.

? likely typing error in family 'x' marker 'x': q = x

Based on sharing at flanking markers, and the value of the error_freq parameter, it is more likely that the data at this marker is a typing error, than for the data to be correct. The q value specifies the increase in likelihood if the data is treated as an error, in log units.

? map degeneracy detected in family %s

If a map contains multiple markers at the same location, and a family has an apparent recombination between colocalized markers, then probability calculations for that family become indeterminate, and the family will be dropped from all likelihood calculations. This message should only be generated when error detection is disabled.

? marker 'x' not defined: data will be ignored.

A data file contains data for the specified marker, however, this name was not defined in the loc array. Marker data for this locus will be skipped.

? invalid disease data for family 'x' person 'x' at file 'x' line x.

The disease status column for this individual does not contain a valid value. The disease status of parents is ignored, so errors will not be reported.

? invalid gender data for family 'x' person 'x' at file 'x' line x.

The gender column does not contain a valid value.

? invalid pedigree data for family 'x' person 'x' at file 'x' line x.

This error can only happen when reading linkage format data. It indicates a formatting error in the father, mother, and gender columns in the input data.

? family 'x' is not a nuclear family at file 'x' line x.

This error can only happen when reading linkage format data. It indicates that either a parent is missing, or the family spans more than two generations.

? inconsistent pedigree structure for family 'x' person 'x' at file 'x' line x.

This indicates that the structure of this family is not the same in different marker data files. For instance, a parent in one file is a sibling in another.

? inconsistent disease data for family 'x' person 'x' at file 'x' line x.

The disease status for this person disagrees with a value read from an earlier data file.

? inconsistent gender data for family 'x' person 'x' at file 'x' line x.

The gender of this person disagrees with a value read from an earlier data file.

? inconsistent data for marker 'x' for family 'x' person 'x' at file 'x' line x.

Two input files both contain allele data for the specified marker for this person, and the data does not agree.

? not enough data at file 'x' line x.

The specified line did not have the expected number of allele identifiers. Verify that the number of alleles specified in the header line agrees with the number of columns of marker data.

? too much data at file 'x' line x.

The specified line was processed successfully, but after all expected data had been read, there were some non-blank characters left over. Verify that the number of alleles specified in the header line agrees with the number of columns of marker data.

? family 'x' person 'x' is male but has two alleles at 'x'.

This error can only happen when reading sex-linked data. Males should either be coded as homozygous at all loci (in linkage format), or using the special `Y' allele to indicate the Y chromosome (either format).