Stuck when almost done: it blocks when "Finished Annotation" appears

[Piccetteeno]

Hello,

The tool performs pretty well (except for " SEVERE: java.nio.file.NoSuchFileException: data/omim_mode.txt" error, which i solved looking at the other issues) but when "Finished Annotation" appears it stuks for more then 12h on the same sample without doing nothing (a java process with 40gb busy RAM keeps going for all the time).
cmd line is:
for F in *.vcf ; do phenomenet-vp -f "$F" -p HP:"1",etc... -i recessive -d -og --outfile "$F".out ; done
System is: Ubuntu 14, Java 8, Python 2.7, 48g RAM
when i kill the process i can see that it generated populated .digenic .top and . res files and an empty .oligogenic file.
Is this normal?