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I get the following error when reading data using DEXSeqDataSetFromHTSeq.

dex <- DEXSeqDataSetFromHTSeq( 
  paths, meta, 
  design=~sample+exon+family:exon+condition:exon, 
  flattenedfile="dr.dexseq.gff")

Error in DEXSeqDataSetFromHTSeq(paths, meta, design = ~sample + exon +  : 
  Count files do not correspond to the flattened annotation file

The exon counts looks like:

ENSDARG00000000001:001 10
ENSDARG00000000001:002 14
ENSDARG00000000001:003 23
ENSDARG00000000001:004 5
ENSDARG00000000001:005 10

The flat gff looks like:

1 dexseq_prepare_annotation.py aggregate_gene 6408 12027 . - . gene_id "ENSDARG00000099104"
1 dexseq_prepare_annotation.py exonic_part 6408 6641 . - . transcripts "ENSDART00000164359"; exonic_part_number "001"; gene_id "ENSDARG00000099104"
1 dexseq_prepare_annotation.py exonic_part 6642 6643 . - . transcripts "ENSDART00000164359+ENSDART00000158290+ENSDART00000157701"; exonic_part_number "002"; gene_id "ENSDARG00000099104"
1 dexseq_prepare_annotation.py exonic_part 6644 6760 . - . transcripts "ENSDART00000167898+ENSDART00000164359+ENSDART00000158290+ENSDART00000157701"; exonic_part_number "003"; gene_id "ENSDARG00000099104"
1 dexseq_prepare_annotation.py exonic_part 6892 6955 . - . transcripts "ENSDART00000167898+ENSDART00000164359+ENSDART00000158290+ENSDART00000157701"; exonic_part_number "004"; gene_id "ENSDARG00000099104"
1 dexseq_prepare_annotation.py exonic_part 6956 7335 . - . transcripts "ENSDART00000158290"; exonic_part_number "005"; gene_id "ENSDARG00000099104"
1 dexseq_prepare_annotation.py exonic_part 9558 9694 . - . transcripts "ENSDART00000167898+ENSDART00000164359+ENSDART00000157701"; exonic_part_number "006"; gene_id "ENSDARG00000099104"

As far as I can see, everything looks fine. Any idea on what might be wrong?