I just ran into this issue with a self-compiled jar file and confirmed
that I have the same issue with ditaa on Debian.  Checking the
binfmt_misc configuration may be useful.  To see what interpreters will
be tried by binfmt_misc, run `/usr/sbin/update-binfmts --find
/usr/bin/ditaa`.  Then try running the interpreter with the jar file
directly (e.g. `/usr/bin/jarwrapper /usr/bin/ditaa`) to see if it works.

If update-binfmts does not print anything, that suggests either
corruption of the JAR file (check `od -An -tx1 -N4
/usr/share/ditaa/ditaa.jar` is `50 4b 03 04`) or that jarwrapper is not
correctly registered (check `/usr/sbin/update-binfmts --display
jarwrapper` prints `jarwrapper (enabled)`).

If update-binfmts prints `/usr/bin/jexec` (or anything else) in addition
to `jarwrapper` and those interpreters do not work, this suggests
conflicting binfmt_misc registrations.  Check the output of `/usr/sbin
/update-binfmts --display` to find out which package installed it.  You
can then remove it by running something like `sudo update-binfmts
--package openjdk-8 --remove jar /usr/bin/jexec`.

The issue, as it appeared on my system, was that the openjdk packages
(e.g. openjdk-8-jre-headless) install /usr/bin/jexec as a binfmt_misc
handler but jexec doesn't work with this jar.  Java version mismatch
perhaps?  I found the issue of jexec/jarwrapper conflict has been raised
before at https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=136993#82
without response.  Perhaps it's time to raise it again?  I'd reassign
this bug to openjdk-8-jre-headless.

** Bug watch added: Debian Bug tracker #136993
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=136993

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https://bugs.launchpad.net/bugs/1498832

Title:
  invalid file (bad magic number): Exec format error

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