Shading signed JAR fails

[jerolba]

Executing benchmarks an exception is raised by the JVM:

Error: A JNI error has occurred, please check your installation and try again
Exception in thread "main" java.lang.SecurityException: Invalid signature file digest for Manifest main attributes
	at java.base/sun.security.util.SignatureFileVerifier.processImpl(SignatureFileVerifier.java:336)
	at java.base/sun.security.util.SignatureFileVerifier.process(SignatureFileVerifier.java:269)
	at java.base/java.util.jar.JarVerifier.processEntry(JarVerifier.java:316)
	at java.base/java.util.jar.JarVerifier.update(JarVerifier.java:230)
	at java.base/java.util.jar.JarFile.initializeVerifier(JarFile.java:752)
	at java.base/java.util.jar.JarFile.getInputStream(JarFile.java:833)
	at java.base/jdk.internal.loader.URLClassPath$JarLoader$2.getInputStream(URLClassPath.java:859)
	at java.base/jdk.internal.loader.Resource.cachedInputStream(Resource.java:77)
	at java.base/jdk.internal.loader.Resource.getByteBuffer(Resource.java:161)
	at java.base/jdk.internal.loader.BuiltinClassLoader.defineClass(BuiltinClassLoader.java:792)
	at java.base/jdk.internal.loader.BuiltinClassLoader.findClassOnClassPathOrNull(BuiltinClassLoader.java:699)
	at java.base/jdk.internal.loader.BuiltinClassLoader.loadClassOrNull(BuiltinClassLoader.java:622)
	at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:580)
	at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:190)
	at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:499)
	at java.base/java.lang.Class.forName0(Native Method)
	at java.base/java.lang.Class.forName(Class.java:374)
	at java.base/sun.launcher.LauncherHelper.loadMainClass(LauncherHelper.java:650)
	at java.base/sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:547)

It is a problem with some of the dependencies which are signed and its descriptor is included in the generated JAR:
http://stackoverflow.com/questions/999489/invalid-signature-file-when-attempting-to-run-a-jar