HTseq count problem

[dietmar13]

hello,

i have a sorted sam file from stampy (paired end) mapped against all viral sequences (multiFA-file) looking like this:
_____________________________
>AC_000001.1
CATCATCAATAATAT...
>AC_000002.1
CATCATCAATAATCT...
...
_____________________________

stampy command:

$stampy/stampy.py --substitutionrate=0.01 -t 20 --sensitive --xcigar -g $index/viruses -h $index/viruses -o out.sam \
	-M $fq1 $fq2

and made an own gtf file from this information like this:
____________________________________________________________
AC_000001.1 virus genome 1 33034 . . . gene_id "AC_000001.1";
AC_000002.1 virus genome 1 34446 . . . gene_id "AC_000002.1";
AC_000003.1 virus genome 1 30536 . . . gene_id "AC_000003.1";
____________________________________________________________


now I want count all mapped read-pairs, which map both to one virus genome (i.e. multiFA-entry):

htseq-count -m union -s no -t genome -i gene_id $sam $gff > ${name}.count

why do i get this error:

Error occured in line 1 of file /home/ws/Data/Oncotest/fa/viral_genome_sorted.fa/viral_genome.GFF.
Error: [Errno 20] Not a directory: '/home/ws/Data/Oncotest/fa/viral_genome_sorted.fa/viral_genome.GFF'
[Exception type: IOError, raised in __init__.py:45]

what could be the problem?

thank you in advance...

dietmar