I am trying to use DEXSeq to analyze a mouse paired-end stranded RNA-seq data (poly-A RNA capture). I Aligned the reads using STAR and obtained the reference genome and annotation file (which I collapsed with dexseq_prepare_annotation.py) from GENCODE (release m11). I used HTSeq to count exons (using command "htseq-count -m union -s reverse -i gene_id -t exon) and over 80% mapped to a feature. 

I set up my countFiles, collapsed annotation file and sampleTable in R:
countFiles <- list.files(directory, pattern=".txt", full.names = TRUE)
sampleTable <- data.frame(row.names = c("WT_RNA_1", "WT_RNA_2", "WT_RNA_3", "KO_RNA_1", "KO_RNA_2", "KO_RNA_3"), condition = c("WT", "WT", "WT", "KO", "KO", "KO"), libType = c("paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end"))

When I try to create a DEXSeqdataset it gives me an out of bounds error:
dxd <- DEXSeqDataSetFromHTSeq(countFiles, sampleData = sampleTable, design= ~sample + exon + condition:exon, flattenedfile = flattenedFile)
Error in FUN(X[[i]], ...) : subscript out of bounds

I have looked over the count files and the collapsed annotation and I can't seem to figure out where the mismatch between these files is occurring. What is curious is that I do not see this error when I use DEXSeq to analyze RNA-seq data from human cell lines. Is there something I am missing regarding alignment and counting of the mouse data set?

Thank you for your help