Failed to start adb -- APK doesn't start after rebuilding with apktool

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I have APK file, I drop it with mouse to my android emulator, it loads successfully. Then I use following commands to repack APK:

apktool d -s app-debug.apk

cd app-debug

apktool b

I get this error when I drag and drop new APK file. I need -s key to preserve .dex file (I need to replace DEX, but I have same problem when replace) and avoid decompile/compile step:

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Stepan Yakovenko On BEST ANSWER

For me uninstalling previous version of application helped. Using adb from command line helped to identify error message.