I'm running kissDE on the results obtained from KisSplice. I used 4 paired-end samples as input for KisSplice, with each of the 8 FQ files totaling ~ 13 gigabytes each.
Using R on a high performance computer cluster, kissDE ran for ~12 days, before reaching this error during the 'diffExpressedVariants' step:
res<-diffExpressedVariants(snp, species, pvalue=1)
 "Pre-processing the data..."
 "Trying to fit models on data..."
 "Searching for best model and computing pvalues..."
 "Error in data.frame(..., check-names = FALSE): arguments imply differing number of rows: 537429
Is any one able to provide more information on this error? Any info would be appreciated.