Using glDepthFunc and transparency in OpenGL

Question

This image is rendered using three passes.

1. In the first pass, I render a three axis.
2. in the second pass a transparent cylinder is rendered (glEnable(GL_BLEND)) alpha = 0.5f.
3. finally the golden and grey spheres are rendered in the third pass(glEnable(GL_BLEND)).

The alpha value of the golden spheres = 1.0f and the grey sphere = 0.2f.

The problem: As you can see,

1. the cylinder overlaps the spheres even though we enable blending.
2. the axes overlap the cylinder and the spheres!

Here is my code:

    glClearColor(1.0f, 1.0f, 1.0f, 1.0f);
    glClearDepthf(1.0f);
    glEnable(GL_DEPTH_TEST);
    glDepthFunc(GL_LEQUAL);
    glClear( GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT );
    glEnable(GL_CULL_FACE);
    glFrontFace(GL_CCW);
    glBlendFunc (GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);

here the data is prepared and sent to shaders (first pass)

    glDrawElements(GL_POINTS, 256, GL_UNSIGNED_INT, reinterpret_cast<void*>(0));

ps: a geometry shader is used to render lines from the given points.

Then we prepare and pass the cylinder data

    glEnable(GL_BLEND);
    glCullFace(GL_FRONT);
    glDrawElements(GL_POINTS, 256, GL_UNSIGNED_INT, reinterpret_cast<void*>(0));
    glCullFace(GL_BACK);
    glDrawElements(GL_POINTS, 256, GL_UNSIGNED_INT, reinterpret_cast<void*>(0));
    glDisable( GL_BLEND);

ps: a geometry shader, also, is used to render the mesh of the cylinders from the given points.

Finally, I render the golden sphere and the grey sphere in one pass

    glEnable(GL_BLEND);
    glDrawElements(GL_LINE_STRIP, goldenSphereNumber, GL_UNSIGNED_INT, (void*)0);
    glDrawElements(GL_LINE_STRIP, sphereIndexCount, GL_UNSIGNED_INT, (void*)0);
    glDisable( GL_BLEND);

ps: here also a geometry shader is used to render the mesh of the cylinders from the given lines.

Do you see any wrong? Could you help, please?