Mesh of a 3D geometry defined by stl files - PLC Error: A segment and a facet intersect at point

Dear Professor Geuzaine,

I have been trying to generate a 3D mesh in the geometry of a coronary vessel enclosed by three stl files for a project.

More specifically I received the geometry of the vessel as a vtk file (which I converted into an .stl file) with both ends open. Using Meshlab I filled both ends and then I extracted both cap fillings from the main vessel (using paraview) in order to have three seperate surfaces into Gmsh so that I can prescribe Boundary Conditions (inlet / outlet / wall).

I merge the three surfaces into Gmsh, I add a volume (elementari entities) where the main surface is the volume and the two caps are the holes, and then using physical groups I prescribe surface (big cap - inlet, small cap - outlet, main vessel - wall) and volume (the added volume - as fluid groups). However when I try to generate a 3D Mesh the Following Error appears: PLC Error: A segment and a facet intersect at a point.

I am new to Gmsh and I have been stuck at this issue for a couple of weeks now. I am mainly using the GUI in order to generate the mesh. I have tried other ways like importing the geometry as one stl file and using filter to generate different surfaces where I am facing other problems. I attach the geo file and the stl files002-LAD-3D-smt-re.stl

big_hole_fill.stlcoronaryb.geo

small_hole_fill.stl

I understand the quality of the triangles on the caps may not be the best, I am not sure if this has an share on the problem.I think there has been a similar problem reported which could be solved by adding Coherence I have not made it work.

Thank you very much for your time.

P.S. Sorry I could not post the issue and attach the files all at once.