Hi Ekaterina,
did you first edit the setup script and run it from the PESTICA directory?  There is a script "setup_pestica.sh" that you have to modify to contain the correct MATLAB_AFNI_DIR (the location of the AFNI MATLAB distribution, unzipped) and PESTICA_DIR (the location where you downloaded and unzipped pestica), and then you have to select the right PESTICA_VOL - the default is usually the right one (16mm^3), and then you have to run this script once from the pestica directory.  Doing this will setup softlinks to the appropriate resp/card_mean_mni.nii files.  Actually, it looks like you have done this, but possibly with an incorrect PESTICA_DIR setup.  The 3dAllineate command that is called from run_pestica_est.sh looks in $PESTICA_DIR/ for the resp_mean_mni.nii file and it looks like you have PESTICA_DIR set to "..".  Can you tell me what this variable is set to?  It should be the location of your pestica distribution.  I would also like to know, do you also have a resp_mean_mni.nii file in your pestica distribution?
Erik