When using HTseq-count I get an warning at the beguining :

    Warning: Read SRR1503280.2 claims to have an aligned mate which could not be found in an adjacent line.

and at the end of the sam file:

    74100000 SAM alignment record pairs processed.
    74200000 SAM alignment record pairs processed.
    74300000 SAM alignment record pairs processed.
    74400000 SAM alignment record pairs processed.

    Error occured when processing SAM input (line 74468230 of file accepted_hits_filtsort_Controle.sam):
      'pair_alignments' needs a sequence of paired-end alignments
      [Exception type: ValueError, raised in __init__.py:603]

and my outputfiles were empty:

    0       HTseq_Controle_output.txt
    0       HTseq_Huntington_Output.txt

I use this code :

    python ~/programs/HTSeq-0.6.1/scripts/htseq-count accepted_hits_filtsort_Controle.sam \
        ~/database/Mus_musculus.primary.gtf > HTseq_Controle_output.txt

I am very newbie but, I really try to look at all the other similar problems people already posted in the past and could not find a solution. Maybe it is trivial and I only need a tip. Could some one help me?
To separate out alignments from paired-end datasets and single-end datasets just use samtools:

    samtools view -bf 1 foo.bam > foo.paired-end.bam
    samtools view -bF 1 foo.bam > foo.single-end.bam

That should suffice. You could also just pipe that into htseq-count.