[BioC] DEXSeq error: Count files do not correspond to the flattened annotation file

[Darwin Sorento Dichmann]

Greetings, 

I created the count files using dexseq_count.py according to the instructions. However, when I attempt to create ExonCountSets using read.HTSeqCounts I get the following error:
---
Error in read.HTSeqCounts(countfiles = file.path(inDir, countfiles), design = tra2bdata,  : 
  Count files do not correspond to the flattened annotation file
---
I *know* that the ecs files corresponds to the flat GFF and I have rerun that step thrice. So, I assume that the error message is really about something else and I would appreciate any help at getting to it. 

FWIW, DEXSeq works on the same data set, but with a slightly different flat GFF (the one that gives me trouble have been changed the gene names). The GFF is flattened from a Cufflinks GTF. 

This is the minimal code that reproduce the error:
# R version 2.15.2 (2012-10-26) -- "Trick or Treat"
# Load DEXSeq and setwd.
source("http://bioconductor.org/biocLite.R")
biocLite("DEXSeq")
library(DEXSeq)
setwd("~/Dropbox/DEXSeq_tra2b_Named/")

# Create data frame of tra2b experimental setup:
sampleID <- c("CTR1","CTR2","CTR3","TRA1","TRA2","TRA3")
condition <-c(rep("uninjected", 3), rep("tra2bMO2", 3))
type <- c(rep("paired-end", 6))
stage<- c(rep("14", 6))
tra2bdata <- data.frame(condition, type, stage, row.names = sampleID)

# Put paths to files into variables.
inDir <- file.path("~/Dropbox/DEXSeq_tra2b_Named/") # Directory to files.
countfiles <- list.files(inDir, pattern = ".txt") # Path to exon count files from HT-Seq.
annotationTra <- file.path( "~/Dropbox/DEXSeq_tra2b_Named/flat_frog_q1_fixed_v2.gff") 

# Create the ExonCountSet. This is where things go wrong.
traExons <- read.HTSeqCounts(countfiles = file.path(inDir, countfiles), 
                                   design = tra2bdata,
                                   flattenedfile = annotationTra)
---
Error in read.HTSeqCounts(countfiles = file.path(inDir, countfiles), design = tra2bdata,  : 
  Count files do not correspond to the flattened annotation file
---

Any help is greatly appreciated. 
Best,
Darwin
________________________________
Darwin Sorento Dichmann, M.S., PhD
University of California, Berkeley
Harland Lab
Molecular and Cell Biology
571 Life Sciences Addition
Berkeley, CA 94720
Phone# (510) 643-7830
E-mail: dichmann at berkeley.edu

Please send Fedex packages to:
163 Life Sciences Addition, attn: Harland lab room 571