Android : Unable to clean project in Android Studio

OS version: Ubuntu 14.04 LTE 64 Bit

Java JRE/JDK version: Oracle JDK 1.8.0_11

Project directory is on a NTFS based drive.

Whenever I try to clean my project I get something like below.

:app:clean FAILED Error:Execution failed for task ':app:clean'.

Unable to delete file: /media/DriveA/AndroidStudioWorkspace/DNA/app/build/intermediates/classes/debug/.../mechandising/MerchandizingActivity$3.class

When I try to delete the build folder manually I get the following error.

Error when getting information for file '/media/DriveA/AndroidStudioWorkspace/DNA/app/build/intermediates/pre-dexed': Input/output error

I am unable to figure out whether its a Linux problem or a Studio problem. I don't face such a problem in Eclipse (Same Drive) so I am just considering it to be something wrong with my studio.

Any Suggestions??