I've already searched a lot about it and I'm aware of both questions "No room for a new \read" with writing a journal and No room for a new \read/\write. Still, I couldn't find a solution to my problem since I'm using the SVG package to include .svg files. The package morewrites helped stopping "No room for a new \write" error messages while e-Tex extensions didn't help with \read (also mentioned here). The include command is entered as follows:
The clean option remove the temporary files produced when extracting pdf from svg.
It turned out that the extraction and the cleaning option are producing the problem (removing them turned off the error messages!).
Having a quick look at the SVG implementation, it appears that calling these options invokes more \immediate\write18 commands. I'm not sure if this command was producing the reading error, but if so, I cannot see how a writing command would request a reading one!