I am currently working with a program that generates aritificial FASTQ files when given a reference genome called Artificial FASTQ Generator. [Here][1] is a link to the description of the program and [here][2] is the manual, it says that the program generates paired-end reads (and it does generate two FASTQ files). After aligning the artificial reads (the two FASTQ files generated by Artificial FASTQ Generator) to the reference genome as paired-end reads using Bowtie 2 I got the following result:

```
  892589 (100.00%) were paired; of these:
    892585 (100.00%) aligned concordantly 0 times
    4 (0.00%) aligned concordantly exactly 1 time
    0 (0.00%) aligned concordantly >1 times
    ----
    892585 pairs aligned concordantly 0 times; of these:
      870486 (97.52%) aligned discordantly 1 time
    ----
    22099 pairs aligned 0 times concordantly or discordantly; of these:
      44198 mates make up the pairs; of these:
        7154 (16.19%) aligned 0 times
        15716 (35.56%) aligned exactly 1 time
        21328 (48.26%) aligned >1 times
99.60% overall alignment rate
```

After aligning both FASTQ files as single end reads, I got the following:

```
  1785178 (100.00%) were unpaired; of these:
    7154 (0.40%) aligned 0 times
    1755694 (98.35%) aligned exactly 1 time
    22330 (1.25%) aligned >1 times
99.60% overall alignment rate
```

What I do not understand is why these reads are aligning as single-end reads and not as paired-end reads as expected? Is anybody familiar with both programs that can help explain this?

EDIT:

Here are the outputs:

 - [1st FASTQ output of AFG][3]
 - [2nd FASTQ output of AFG][4]
 - [SAM output of Bowtie 2][5] (single-end alignment)

EDIT 2:

Here is the output of the paired-end alignment.

[SAM output of Bowtie 2][6] (paired-end alignment)

 [1]: http://sourceforge.net/projects/artfastqgen/
 [2]: http://sourceforge.net/p/artfastqgen/wiki/Home/
 [3]: https://drive.google.com/file/d/0B3xfexs8wgRTS2tiYkROanJYdnM/edit?usp=sharing
 [4]: https://drive.google.com/file/d/0B3xfexs8wgRTRWdxeV9iZkhoOGc/edit?usp=sharing
 [5]: https://drive.google.com/file/d/0B3xfexs8wgRTOVV2Rl9KSUxSc3c/edit?usp=sharing
 [6]: https://drive.google.com/file/d/0B3xfexs8wgRTR1NDM3A3TE5JX2c/edit?usp=sharing
Maybe you should post an example of the output, a few read pairs should be sufficient.

There could be many reasons, e.g.:

 - Bug or wrong use of the simulator: mate pairs not on complementary strands
 - too large insert size
 - Bug: annotated pairs do not pair
 - too low simulated quality scores (single-end do align though, so not in this case)
 - too high simulated error rate (dto.)

Maybe you should use a simulator that is better tested, see:

https://www.biostars.org/p/2194/