I finally got it right! Thank you guys! I made a mistake while setting the ".bashrc" I configured "$NTA=/home/myusername/nupic/nta/eng". So in the end the folder gets deleted (in a cleanup step I guess) because it's not supposed to be there. It´s a really stupid mistake, but now is working perfectly.
This was the guide I was following: https://github.com/numenta/nupic/wiki/Installing-NuPIC-on-Ubuntu I'm using Debian and it's a pretty straight forward guide. Thanks again to everyone that answered :)
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