Hey @arushib30,
From your description of the issue, it seems it may be related to resource allocation as you said the workflow runs fine when you pass in less files, and it seems to break when you try to run it on all 12. I would try specifying more resource allocation and see if it fixes the issue you are running into.
Here is a post on how to increase memory on KNIME:
https://forum.knime.com/t/change-memory-on-knime-ini/43472/5
Hope this helps,
TL