I've created another binary called gasic-examples and moved all examples there.
I ran the tests again, and they all pass in my chroot. I also rebuilt the chroot in case there was something wrong there, and turns out they still pass. I also tried adding:
bowtie-build dwv.fasta dwv.fasta
to the autopkgtests for the bowtie package, and all of those pass too.
For the purpose of completing autopkgtests for gasic, I have tried to circumvent this issue by changing the mapper for gasic from bowtie to bwa, so bowtie will no longer be required for testing gasic.
I've also fixed a patch and added some more tests.
Please take a look - specially at the new binary (in case I've misplaced some file) - and if these tests work now, please sponsor.
Regarding bowtie, I'm unable to reproduce the issue, so if you have any ideas that I can try, please let me know.