This is the result from the dry_run option:

[xl@localhost sb23]$ align_epi_anat.py -anat sb23_mpra+orig -epi epi_r03+orig -epi_base 5 -ex_mode dry_run
#++ align_epi_anat version: 1.06
#Would be running:
cd /home/xl/AFNI_data4/sb23
3dAttribute DELTA /home/xl/AFNI_data4/sb23/epi_r03+orig
#++ Spacing for EPI to tlrc alignment is 1.234567
#Would be running:
cd /home/xl/AFNI_data4/sb23
3dAttribute DELTA /home/xl/AFNI_data4/sb23/sb23_mpra+orig
#++ Spacing for anat to EPI deobliquing is 1.234567 mm
#++ Removing all the temporary files
#Would be running:
cd /home/xl/AFNI_data4/sb23
rm -f __tt_epi_r03*
#Would be running:
cd /home/xl/AFNI_data4/sb23
rm -f __tt_sb23_mpra*
#Would be running:
cd /home/xl/AFNI_data4/sb23
3dcopy /home/xl/AFNI_data4/sb23/sb23_mpra+orig __tt_sb23_mpra
#++ Removing skull from anatomical data
#Would be running (command trimmed):
cd /home/xl/AFNI_data4/sb23
3dSkullStrip -input __tt_sb23_mpra+orig -prefix __tt_sb23_mpra_ns
#Would be running (command trimmed):
cd /home/xl/AFNI_data4/sb23
3dinfo __tt_sb23_mpra_ns+orig | grep 'Data Axes Tilt:'|grep 'Oblique'
#++ Matching obliquity of anat to epi
#Would be running (command trimmed):
cd /home/xl/AFNI_data4/sb23
3dWarp -verb -card2oblique epi_r03+orig -prefix __tt_sb23_mpra_ns_ob -newgrid 1.234567 __tt_sb23_mpra_ns+orig | grep -A 4 '# mat44 Obliquity Transformation ::' > __tt_sb23_mpra_ns_obla2e_mat.1D
#Would be running:
cd /home/xl/AFNI_data4/sb23
3dAttribute TAXIS_OFFSETS /home/xl/AFNI_data4/sb23/epi_r03+orig
#++ Correcting for slice timing
#Would be running (command trimmed):
cd /home/xl/AFNI_data4/sb23
3dTshift -prefix __tt_epi_r03_tsh_al -cubic epi_r03+orig
#++ Volume registration for epi data
#Would be running (command trimmed):
cd /home/xl/AFNI_data4/sb23
3dvolreg -1Dfile epi_r03_tsh_vr_al_motion.1D -1Dmatrix_save epi_r03_tsh_vr_al_mat.aff12.1D -prefix epi_r03_tsh_vr_al -base 5 -cubic __tt_epi_r03_tsh_al+orig
#++ Creating representative epi sub-brick
#Would be running (command trimmed):
cd /home/xl/AFNI_data4/sb23
3dbucket -prefix __tt_epi_r03_tsh_vr_ts_al epi_r03_tsh_vr_al+orig'[5]'
#++ resampling epi to match anatomical data
#Would be running (command trimmed):
cd /home/xl/AFNI_data4/sb23
3dresample -master __tt_sb23_mpra_ns_ob+orig -prefix __tt_epi_r03_tsh_vr_ts_rs_al -inset __tt_epi_r03_tsh_vr_ts_al+orig -rmode Cu
#++ removing skull or area outside brain
#Would be running (command trimmed):
cd /home/xl/AFNI_data4/sb23
3dSkullStrip -input __tt_epi_r03_tsh_vr_ts_rs_al+orig -prefix __tt_epi_r03_tsh_vr_ts_rs_ns_al
#++ Computing weight mask
#Would be running (command trimmed):
cd /home/xl/AFNI_data4/sb23
3dBrickStat -automask -percentile 90.000000 1 90.000000 __tt_epi_r03_tsh_vr_ts_rs_ns_al+orig
#++ Would be applying threshold for real run here
#Would be running (command trimmed):
cd /home/xl/AFNI_data4/sb23
3dcalc -datum float -prefix __tt_epi_r03_tsh_vr_ts_rs_ns_al_wt -a __tt_epi_r03_tsh_vr_ts_rs_ns_al+orig -expr 'min(1,(a/-999.000000))'
#++ Aligning anatomical data to epi data
#Would be running (command trimmed):
cd /home/xl/AFNI_data4/sb23
3dAllineate -lpc -wtprefix __tt_sb23_mpra_ns_ob_al_wtal -weight __tt_epi_r03_tsh_vr_ts_rs_ns_al_wt+orig -source __tt_sb23_mpra_ns_ob+orig -source_automask+4 -prefix __tt_sb23_mpra_ns_ob_temp_al -base __tt_epi_r03_tsh_vr_ts_rs_ns_al+orig -cmass+xy -1Dmatrix_save sb23_mpra_al_a2e_only_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff
#Would be running:
cd /home/xl/AFNI_data4/sb23
cat_matvec -ONELINE sb23_mpra_al_a2e_only_mat.aff12.1D __tt_sb23_mpra_ns_obla2e_mat.1D > sb23_mpra_al_mat.aff12.1D
#++ Combining anat to epi and oblique transformations
#Would be running (command trimmed):
cd /home/xl/AFNI_data4/sb23
3dAllineate -base __tt_epi_r03_tsh_vr_ts_rs_ns_al+orig -1Dmatrix_apply sb23_mpra_al_mat.aff12.1D -prefix sb23_mpra_al -input sb23_mpra+orig -master SOURCE
#++ Creating final output: skullstripped anatomical data
#Would be running:
cd /home/xl/AFNI_data4/sb23
3dcopy /home/xl/AFNI_data4/sb23/__tt_sb23_mpra_ns_ob+orig sb23_mpra_ns_al
#++ Creating final output: anat data aligned to epi data
# copy is not necessary
#++ Creating final output: time-shifted epi
#Would be running:
cd /home/xl/AFNI_data4/sb23
3dcopy /home/xl/AFNI_data4/sb23/__tt_epi_r03_tsh_al+orig epi_r03_tshft_al
#++ Creating final output: time series volume-registered epi
#Would be running:
cd /home/xl/AFNI_data4/sb23
3dcopy /home/xl/AFNI_data4/sb23/epi_r03_tsh_vr_al+orig epi_r03_vr_al
#++ Removing all the temporary files
#Would be running:
cd /home/xl/AFNI_data4/sb23
rm -f __tt_epi_r03*
#Would be running:
cd /home/xl/AFNI_data4/sb23
rm -f __tt_sb23_mpra*

# Finished alignment successfully


I think the original error stems from the script trying to remove the file(s) __tt_epi_r03*, which doesn't exist. (from the line "rm -f __tt_epi_r03*" prior to the Traceback of errors, from my first post). Is there any reason you can think of as to why this failed to be created in the process? Thanks.