I've used APT to process the CEL files to generate the cross-marker normalized signal intensity data from Axiom Genome-wide Chicken Array (Affymetrix).

I've used this following command:

apt-probeset-genotype \
  -c Axiom_GW_GT_Chicken.r1.cdf \
  -a birdseed \
  --read-models-birdseed Axiom_GW_GT_Chicken.r1.AxiomGT1.models \
  --special-snps Axiom_GW_GT_Chicken.r1.specialSNPs \
  --out-dir apt \
  --cel-files animal.txt

When I ran this command, the program exited with a fatal error:

FATAL ERROR:Exception. msg: 'Missing required column: ' source file: 'PriorsReader.cpp:352'

Could someone help me to fix this problem?

Thanks