title: Running a jar file on unix (FileNotFoundException) Error due to slash inconsistency
body: <p>I don't have any experience working with Java (just basic knowledge), and I am trying to run a Jar file on Unix system.
  so I figured out how to run the file using the following command:</p>
  <pre><code>java -Xmx80000m -jar ProCon.jar -conv=PD1x -pks=Consensus [...and some other arguments...]
  </code></pre>
  <p>Note that I am running the jar file from my account on a cluster. So my path would be something like this:</p>
  <pre><code>scratch/user/ProCon/
  </code></pre>
  <p>The app starts running, however, I guess it gets confused to link to its resources as it throughs some errors and warnings:</p>
  <blockquote>
  <p>java.io.FileNotFoundException: .\resources\obofiles\unimod.obo (No
  such file or directory)</p>
  </blockquote>
  <p>or</p>
  <blockquote>
  <p>/scratch/user/ProCon\resources\taxonomy_ID_names.txt</p>
  </blockquote>
  <p>in the example above, it seems as if the jar file reads my path but adds another path (resources\taxonomy_ID_names.txt) with a wrong slash, causing the model to get confused with the path and slashes.
  is there any way to fix such issues?</p>
  <p>The program I am using is P<a href="http://www5.rz.ruhr-uni-bochum.de:8666/mpc/software/ProCon/index.html.en" rel="nofollow noreferrer">ROTEOMICS CONVERSION TOOL (PROCON)</a>. It can be downloaded from <a href="http://www5.rz.ruhr-uni-bochum.de:8666/mpc/mam/content/Software/ProCon/procon_dist-0.9.804.zip" rel="nofollow noreferrer">THIS LINK: PROCON</a></p>