diff --git a/scripts/ANALYSIS.anasum.sh b/scripts/ANALYSIS.anasum.sh
index 7b58e593..07801675 100755
--- a/scripts/ANALYSIS.anasum.sh
+++ b/scripts/ANALYSIS.anasum.sh
@@ -87,8 +87,8 @@ sed -e "s|FILELIST|$FLIST|" \
 chmod u+x "$FSCRIPT.sh"
 echo "$FSCRIPT.sh"
 
-SUBC="$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh"
-# run locally or on cluster
+SUBC=`$( dirname "$0" )/helper_scripts/UTILITY.readSubmissionCommand.sh`
+# run locally or on cluster (expand shell variables in submission string)
 SUBC=`eval "echo \"$SUBC\""`
 if [[ $SUBC == *"ERROR"* ]]; then
     echo "$SUBC"
@@ -113,5 +113,3 @@ elif [[ $SUBC == *parallel* ]]; then
 elif [[ $SUBC == *simple* ]]; then
 	"$FSCRIPT.sh" |& tee $FSCRIPT.log
 fi
-
-exit
diff --git a/scripts/ANALYSIS.anasum_allcuts.sh b/scripts/ANALYSIS.anasum_allcuts.sh
index b7dbe2e4..cc6cc2a6 100755
--- a/scripts/ANALYSIS.anasum_allcuts.sh
+++ b/scripts/ANALYSIS.anasum_allcuts.sh
@@ -63,7 +63,7 @@ do
         fi
         echo $CDIR
         mkdir -p "$TMPDIR/${CDIR}"
-        ./ANALYSIS.anasum_parallel_from_runlist.sh ${RUNL} \
+        $(dirname "$0")/ANALYSIS.anasum_parallel_from_runlist.sh ${RUNL} \
             "$TMPDIR/${CDIR}" \
             ${C} \
             ${IGNORETYPE} \
@@ -71,7 +71,7 @@ do
             $PREDIR $SKIPIFPROCESSED | tee -a ${TMPLOG}
     elif [[ $RUNTYPE == "V2DL3" ]]; then
         mkdir -p "$TMPDIR/v2dl3_${C}"
-         ./ANALYSIS.v2dl3.sh ${RUNL} \
+         $(dirname "$0")/ANALYSIS.v2dl3.sh ${RUNL} \
              "$TMPDIR/v2dl3_${C}" \
              ${C} | tee -a ${TMPLOG}
     else
diff --git a/scripts/ANALYSIS.anasum_combine.sh b/scripts/ANALYSIS.anasum_combine.sh
index 17a54e20..093928d8 100755
--- a/scripts/ANALYSIS.anasum_combine.sh
+++ b/scripts/ANALYSIS.anasum_combine.sh
@@ -76,6 +76,15 @@ SUBSCRIPT=$( dirname "$0" )"/helper_scripts/ANALYSIS.anasum_combine_sub"
 FSCRIPT="$LOGDIR/anasum_combine-$DATE-RUN$RUN-$(date +%s)"
 echo "Run script written to $FSCRIPT"
 
+# Check that anasum output files exist before combining
+NANASUMFILES=$(find "$DDIR" -maxdepth 1 -name "*.anasum.root" | wc -l)
+if [[ $NANASUMFILES -eq 0 ]]; then
+    echo "Error: no .anasum.root files found in $DDIR"
+    echo "Run ANALYSIS.anasum_parallel_from_runlist.sh and wait for completion before combining."
+    exit 1
+fi
+echo "Found $NANASUMFILES anasum output files in $DDIR"
+
 sed -e "s|RRUNLIST|$RUNLIST|" \
     -e "s|DDDIR|$DDIR|" \
     -e "s|RRUNP|$RUNP|" \
diff --git a/scripts/ANALYSIS.mscw_energy.sh b/scripts/ANALYSIS.mscw_energy.sh
index 82459345..3780ee3c 100755
--- a/scripts/ANALYSIS.mscw_energy.sh
+++ b/scripts/ANALYSIS.mscw_energy.sh
@@ -12,7 +12,7 @@ if [ "$#" -lt 2 ]; then
 echo "
 MSCW_ENERGY data analysis: submit jobs from a simple run list
 
-ANALYSIS.mscw_energy.sh <runlist> [output directory] [evndisp directory] [preprocessing skip] [Rec ID] [ATM]
+ANALYSIS.mscw_energy.sh <runlist> [output directory] [evndisp directory] [preprocessing skip] [Rec ID]
 
 required parameters:
 
@@ -32,9 +32,6 @@ optional parameters:
     [Rec ID]                reconstruction ID. Default 0
                             (see EVNDISP.reconstruction.runparameter)
 
-    [ATM]                   set atmosphere ID (overwrite the value from the evndisp stage)
-
-
 The analysis type (cleaning method; direction reconstruction) is read from the \$VERITAS_ANALYSIS_TYPE environmental
 variable (e.g., AP_DISP, NN_DISP; here set to: \"$VERITAS_ANALYSIS_TYPE\").
 
@@ -60,7 +57,6 @@ RUNLIST=$1
 [[ "$3" ]] && INPUTDIR=$3 || INPUTDIR="$VERITAS_PREPROCESSED_DATA_DIR/${VERITAS_ANALYSIS_TYPE:0:2}/evndisp"
 [[ "$4" ]] && SKIP=$4 || SKIP=1
 [[ "$5" ]] && ID=$5 || ID=0
-[[ "$6" ]] && FORCEDATMO=$6
 DISPBDT="1"
 
 # Read runlist
diff --git a/scripts/ANALYSIS.v2dl3.sh b/scripts/ANALYSIS.v2dl3.sh
index c0f2ab79..77f3cad5 100755
--- a/scripts/ANALYSIS.v2dl3.sh
+++ b/scripts/ANALYSIS.v2dl3.sh
@@ -54,7 +54,7 @@ DATE=`date +"%y%m%d"`
 LOGDIR="$VERITAS_USER_LOG_DIR/V2DL3-${DATE}-$(uuidgen)/"
 mkdir -p "$LOGDIR"
 echo -e "Log files will be written to:\n $LOGDIR"
-rm -f ${LOGIDR}/x* 2>/dev/null
+rm -f ${LOGDIR}/x* 2>/dev/null
 
 # split run list into smaller run lists
 sort -u "${RUNLIST}" -o "${LOGDIR}/$(basename "${RUNLIST}")"
@@ -98,11 +98,11 @@ do
             JOBID=$( echo "$JOBID" | grep -oP "Your job [0-9.-:]+" | awk '{ print $3 }' )
         fi
 
-        echo "RUN $AFILE JOBID $JOBID"
-        echo "RUN $AFILE SCRIPT $FSCRIPT.sh"
+        echo "RUN $J JOBID $JOBID"
+        echo "RUN $J SCRIPT $FSCRIPT.sh"
         if [[ $SUBC != */dev/null* ]] ; then
-            echo "RUN $AFILE OLOG $FSCRIPT.sh.o$JOBID"
-            echo "RUN $AFILE ELOG $FSCRIPT.sh.e$JOBID"
+            echo "RUN $J OLOG $FSCRIPT.sh.o$JOBID"
+            echo "RUN $J ELOG $FSCRIPT.sh.e$JOBID"
         fi
     elif [[ $SUBC == *condor* ]]; then
         $(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh $FSCRIPT.sh $h_vmem $tmpdir_size
@@ -116,7 +116,7 @@ do
         $SUBC $FSCRIPT.sh
     elif [[ $SUBC == *parallel* ]]; then
         echo "$FSCRIPT.sh &> $FSCRIPT.log" >> "$LOGDIR/runscripts.$TIMETAG.dat"
-        echo "RUN $AFILE OLOG $FSCRIPT.log"
+        echo "RUN $J OLOG $FSCRIPT.log"
     elif [[ "$SUBC" == *simple* ]] ; then
 	    "$FSCRIPT.sh" |& tee "$FSCRIPT.log"
 	fi
diff --git a/scripts/IRF.combine_lookup_table_parts.sh b/scripts/IRF.combine_lookup_table_parts.sh
index f7cc1fe3..f4a43197 100755
--- a/scripts/IRF.combine_lookup_table_parts.sh
+++ b/scripts/IRF.combine_lookup_table_parts.sh
@@ -74,7 +74,7 @@ echo -e "Output files will be written to:\n $ODIR"
 mkdir -p "$ODIR"
 chmod g+w "$ODIR"
 
-if [[ -f $OFILE ]]; then
+if [[ -f "$ODIR/$OFILE" ]]; then
     echo "ERROR: table file $ODIR/$OFILE exists; move it or delete it"
     exit 1
 fi
diff --git a/scripts/IRF.generate_lookup_table_parts.sh b/scripts/IRF.generate_lookup_table_parts.sh
index 13b8b053..907e00b0 100755
--- a/scripts/IRF.generate_lookup_table_parts.sh
+++ b/scripts/IRF.generate_lookup_table_parts.sh
@@ -112,18 +112,18 @@ if [[ $SUBC == *"ERROR"* ]]; then
     exit 1
 fi
 if [[ $SUBC == *qsub* ]]; then
-    JOBID=`$SUBC $FSCRIPT.sh`
+    JOBID=`$SUBC $FSCRIPT`
     echo "JOBID: $JOBID"
 elif [[ $SUBC == *condor* ]]; then
-    $(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh $FSCRIPT.sh $h_vmem $tmpdir_size
+    $(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh $FSCRIPT $h_vmem $tmpdir_size
     echo "-------------------------------------------------------------------------------"
     echo "Job submission using HTCondor - run the following script to submit jobs:"
     echo "$EVNDISPSCRIPTS/helper_scripts/submit_scripts_to_htcondor.sh ${LOGDIR} submit"
     echo "-------------------------------------------------------------------------------"
 elif [[ $SUBC == *sbatch* ]]; then
-    $SUBC $FSCRIPT.sh
+    $SUBC $FSCRIPT
 elif [[ $SUBC == *parallel* ]]; then
-    echo "$FSCRIPT.sh &> $FSCRIPT.log" >> "$LOGDIR/runscripts.dat"
+    echo "$FSCRIPT &> $FSCRIPT.log" >> "$LOGDIR/runscripts.dat"
 elif [[ "$SUBC" == *simple* ]]; then
-    "$FSCRIPT.sh" | tee "$FSCRIPT.log"
+    "$FSCRIPT" | tee "$FSCRIPT.log"
 fi
diff --git a/scripts/IRF.mscw_energy_MC.sh b/scripts/IRF.mscw_energy_MC.sh
index 8aa705f2..48d9c203 100755
--- a/scripts/IRF.mscw_energy_MC.sh
+++ b/scripts/IRF.mscw_energy_MC.sh
@@ -137,18 +137,18 @@ if [[ $SUBC == *"ERROR"* ]]; then
     exit 1
 fi
 if [[ $SUBC == *qsub* ]]; then
-    JOBID=`$SUBC $FSCRIPT.sh`
+    JOBID=`$SUBC $FSCRIPT`
     echo "JOBID: $JOBID"
 elif [[ $SUBC == *condor* ]]; then
-    $(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh $FSCRIPT.sh $h_vmem $tmpdir_size
+    $(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh $FSCRIPT $h_vmem $tmpdir_size
     echo "-------------------------------------------------------------------------------"
     echo "Job submission using HTCondor - run the following script to submit jobs:"
     echo "$EVNDISPSCRIPTS/helper_scripts/submit_scripts_to_htcondor.sh ${LOGDIR} submit"
     echo "-------------------------------------------------------------------------------"
 elif [[ $SUBC == *sbatch* ]]; then
-    $SUBC $FSCRIPT.sh
+    $SUBC $FSCRIPT
 elif [[ $SUBC == *parallel* ]]; then
-    echo "$FSCRIPT.sh &> $FSCRIPT.log" >> "$LOGDIR/runscripts.dat"
+    echo "$FSCRIPT &> $FSCRIPT.log" >> "$LOGDIR/runscripts.dat"
 elif [[ "$SUBC" == *simple* ]]; then
-    "$FSCRIPT.sh" | tee "$FSCRIPT.log"
+    "$FSCRIPT" | tee "$FSCRIPT.log"
 fi
diff --git a/scripts/IRF.optimizeTMVAforGammaHadronSeparation.sh b/scripts/IRF.optimizeTMVAforGammaHadronSeparation.sh
index 00341f44..7506ef9e 100755
--- a/scripts/IRF.optimizeTMVAforGammaHadronSeparation.sh
+++ b/scripts/IRF.optimizeTMVAforGammaHadronSeparation.sh
@@ -80,6 +80,7 @@ fi
 
 if [[ ! -e $VERITAS_EVNDISP_AUX_DIR/EffectiveAreas/${EFFFILE} ]]; then
     echo "Error - effective area file not found ${EFFFILE}"
+    exit 1
 fi
 if [[ ${EPOCH:0:2} == "V4" ]] || [[ ${EPOCH:0:2} == "V5" ]]; then
     RUNPAR="$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/TMVA.BDT.V4.runparameter"
@@ -88,8 +89,8 @@ else
 fi
 #####################################
 # energy bins
-if grep -q "^* ENERGYBINS" "$RUNPAR"; then
-    ENBINS=$( cat "$RUNPAR" | grep "^* ENERGYBINS 1" | sed -e 's/* ENERGYBINS 1//' | sed -e 's/ /\n/g')
+if grep -q "^\* ENERGYBINS" "$RUNPAR"; then
+    ENBINS=$( cat "$RUNPAR" | grep "^\* ENERGYBINS" | sed -e 's/\* ENERGYBINS//' | sed -e 's/ /\n/g')
     declare -a EBINARRAY=( $ENBINS ) #convert to array
     count1=1
     NENE=$((${#EBINARRAY[@]}-$count1)) #get number of bins
diff --git a/scripts/IRF.production.sh b/scripts/IRF.production.sh
index 61735277..02f766ec 100755
--- a/scripts/IRF.production.sh
+++ b/scripts/IRF.production.sh
@@ -308,7 +308,7 @@ for VX in $EPOCH; do
        if [[ $IRFTYPE == "ANAXGBANGRES" ]]; then
             MSCWDIR="$VERITAS_IRFPRODUCTION_DIR/$EDVERSION/${ANATYPE}/${SIMTYPE}/${VX}_ATM${ATM}_gamma/MSCW_RECID${RECID}_DISP"
             echo "XGB reconstruction reading from $MSCWDIR"
-            ./IRF.dispXGB.sh "stereo_analysis" "${MSCWDIR}" "${MSCWDIR}"
+            $(dirname "$0")/IRF.dispXGB.sh "stereo_analysis" "${MSCWDIR}" "${MSCWDIR}"
             continue
        fi
        #############################################
@@ -316,7 +316,7 @@ for VX in $EPOCH; do
        if [[ $IRFTYPE == "ANAXGBGH" ]]; then
             MSCWDIR="$VERITAS_IRFPRODUCTION_DIR/$EDVERSION/${ANATYPE}/${SIMTYPE}/${VX}_ATM${ATM}_gamma/MSCW_RECID${RECID}_DISP"
             echo "XGB classification reading from $MSCWDIR"
-            ./IRF.dispXGB.sh "classification" "${MSCWDIR}" "${MSCWDIR}"
+            $(dirname "$0")/IRF.dispXGB.sh "classification" "${MSCWDIR}" "${MSCWDIR}"
             continue
        fi
        #############################################
@@ -327,7 +327,7 @@ for VX in $EPOCH; do
            ODIR="$VERITAS_IRFPRODUCTION_DIR/$EDVERSION/${ANATYPE}/${SIMTYPE}/${VX}_ATM${ATM}_gamma/TrainXGBGammaHadron"
            echo "XGB Classification Training"
            echo "${BCKDIR}" "${RUNPAR}" "${ODIR}" "${SIMTYPE}" "${VX}" "${ATM}"
-           ./IRF.trainXGBforGammaHadronSeparationTraining.sh "${BCKDIR}" "${RUNPAR}" "${ODIR}" "${SIMTYPE}" "${VX}" "${ATM}"
+           $(dirname "$0")/IRF.trainXGBforGammaHadronSeparationTraining.sh "${BCKDIR}" "${RUNPAR}" "${ODIR}" "${SIMTYPE}" "${VX}" "${ATM}"
            continue
        fi
        #############################################
@@ -335,54 +335,50 @@ for VX in $EPOCH; do
        # train per epoch and atmosphere and for each cut
        # (cut as sizesecondmax cut is applied)
        if [[ $IRFTYPE == "TRAINTMVA" ]] || [[ $IRFTYPE == "OPTIMIZETMVA" ]]; then
-            for VX in $EPOCH; do
-                for ATM in $ATMOS; do
-                    for C in ${CUTTYPES[@]}; do
-                        echo "Training/optimising TMVA for $C cuts, ${VX} ATM${ATM}"
-                        BDTDIR="$VERITAS_IRFPRODUCTION_DIR/$EDVERSION/${ANATYPE}/BDTtraining"
-                        MVADIR="${BDTDIR}/GammaHadronBDTs_${VX:0:2}/${VX}_ATM${ATM}/${C/PointSource-/}/"
-                        # list of background files
-                        TRAINDIR="${BDTDIR}/mscw_${VX:0:2}/"
-                        if [[ $DISPBDT == "1" ]]; then
-                            TRAINDIR="${BDTDIR}/mscw_${VX:0:2}_DISP/"
-                            MVADIR="${BDTDIR}/GammaHadronBDTs_${VX:0:2}_DISP/${VX}_ATM${ATM}/${C/PointSource-/}/"
-                        fi
-                        mkdir -p -v "${MVADIR}"
-                        if [[ $IRFTYPE == "TRAINTMVA" ]]; then
-                            # retrieve size cut
-                            CUTFIL="$VERITAS_EVNDISP_AUX_DIR"/GammaHadronCutFiles/ANASUM.GammaHadron-Cut-${C}-TMVA-Preselection.dat
-                            echo "CUTFILE: $CUTFIL"
-                            SIZECUT=`grep "* sizesecondmax" $CUTFIL | grep ${EPOCH:0:2} | awk '{print $3}' | sort -u`
-                            if [ -z "$SIZECUT" ]
-                            then
-                                echo "No size cut found; skipping cut $C"
-                                continue
-                            fi
-                            echo "Size cut applied: $SIZECUT"
-                            RUNPAR="TMVA.BDT.runparameter"
-                            if [[ ${EPOCH:0:2} == "V4" ]] || [[ ${EPOCH:0:2} == "V5" ]]; then
-                                cp -f "$VERITAS_EVNDISP_AUX_DIR"/ParameterFiles/TMVA.BDT.V4.runparameter "$MVADIR"/"$RUNPAR"
-                            else
-                                cp -f "$VERITAS_EVNDISP_AUX_DIR"/ParameterFiles/"$RUNPAR" "$MVADIR"/"$RUNPAR"
-                            fi
-                            sed -i "s/TMVASIZECUT/${SIZECUT}/" "$MVADIR"/"$RUNPAR"
-                            if [[ $CUTFIL = *"NTel3"* ]]; then
-                                sed -i "s/NImages>1/NImages>2/" "$MVADIR"/"$RUNPAR"
-                            fi
-                            ./IRF.trainTMVAforGammaHadronSeparation.sh \
-                                         "${TRAINDIR}" \
-                                         "$MVADIR"/"$RUNPAR" \
-                                         "${MVADIR}" BDT ${SIMTYPE} ${VX} "${ATM}"
-                         # Cut optimization
-                         elif [[ $IRFTYPE == "OPTIMIZETMVA" ]]; then
-                             echo "OPTIMIZE TMVA $C ${BDTDIR}/BackgroundRates/${VX:0:2}"
-                             ./IRF.optimizeTMVAforGammaHadronSeparation.sh \
-                                 "${BDTDIR}/BackgroundRates/${VX:0:2}" \
-                                 "${C/PointSource-/}" \
-                                 ${SIMTYPE} ${VX} "${ATM}"
-                         fi
-                    done
-                done
+            for C in ${CUTTYPES[@]}; do
+                echo "Training/optimising TMVA for $C cuts, ${VX} ATM${ATM}"
+                BDTDIR="$VERITAS_IRFPRODUCTION_DIR/$EDVERSION/${ANATYPE}/BDTtraining"
+                MVADIR="${BDTDIR}/GammaHadronBDTs_${VX:0:2}/${VX}_ATM${ATM}/${C/PointSource-/}/"
+                # list of background files
+                TRAINDIR="${BDTDIR}/mscw_${VX:0:2}/"
+                if [[ $DISPBDT == "1" ]]; then
+                    TRAINDIR="${BDTDIR}/mscw_${VX:0:2}_DISP/"
+                    MVADIR="${BDTDIR}/GammaHadronBDTs_${VX:0:2}_DISP/${VX}_ATM${ATM}/${C/PointSource-/}/"
+                fi
+                mkdir -p -v "${MVADIR}"
+                if [[ $IRFTYPE == "TRAINTMVA" ]]; then
+                    # retrieve size cut
+                    CUTFIL="$VERITAS_EVNDISP_AUX_DIR"/GammaHadronCutFiles/ANASUM.GammaHadron-Cut-${C}-TMVA-Preselection.dat
+                    echo "CUTFILE: $CUTFIL"
+                    SIZECUT=`grep "* sizesecondmax" $CUTFIL | grep ${VX:0:2} | awk '{print $3}' | sort -u`
+                    if [ -z "$SIZECUT" ]
+                    then
+                        echo "No size cut found; skipping cut $C"
+                        continue
+                    fi
+                    echo "Size cut applied: $SIZECUT"
+                    RUNPAR="TMVA.BDT.runparameter"
+                    if [[ ${VX:0:2} == "V4" ]] || [[ ${VX:0:2} == "V5" ]]; then
+                        cp -f "$VERITAS_EVNDISP_AUX_DIR"/ParameterFiles/TMVA.BDT.V4.runparameter "$MVADIR"/"$RUNPAR"
+                    else
+                        cp -f "$VERITAS_EVNDISP_AUX_DIR"/ParameterFiles/"$RUNPAR" "$MVADIR"/"$RUNPAR"
+                    fi
+                    sed -i "s/TMVASIZECUT/${SIZECUT}/" "$MVADIR"/"$RUNPAR"
+                    if [[ $CUTFIL = *"NTel3"* ]]; then
+                        sed -i "s/NImages>1/NImages>2/" "$MVADIR"/"$RUNPAR"
+                    fi
+                    $(dirname "$0")/IRF.trainTMVAforGammaHadronSeparation.sh \
+                                 "${TRAINDIR}" \
+                                 "$MVADIR"/"$RUNPAR" \
+                                 "${MVADIR}" BDT ${SIMTYPE} ${VX} "${ATM}"
+                 # Cut optimization
+                 elif [[ $IRFTYPE == "OPTIMIZETMVA" ]]; then
+                     echo "OPTIMIZE TMVA $C ${BDTDIR}/BackgroundRates/${VX:0:2}"
+                     $(dirname "$0")/IRF.optimizeTMVAforGammaHadronSeparation.sh \
+                         "${BDTDIR}/BackgroundRates/${VX:0:2}" \
+                         "${C/PointSource-/}" \
+                         ${SIMTYPE} ${VX} "${ATM}"
+                 fi
             done
             continue
        fi
diff --git a/scripts/IRF.selectRunsForGammaHadronSeparationTraining.sh b/scripts/IRF.selectRunsForGammaHadronSeparationTraining.sh
index 0cc02265..6ed94597 100755
--- a/scripts/IRF.selectRunsForGammaHadronSeparationTraining.sh
+++ b/scripts/IRF.selectRunsForGammaHadronSeparationTraining.sh
@@ -57,7 +57,7 @@ if [[ "${RUNPAR##*.}" == "json" ]]; then
         }
     }')
 else
-    ZEBINS=$( cat "$RUNPAR" | grep "^* ZENBINS " | sed -e 's/* ZENBINS//' | sed -e 's/ /\n/g')
+    ZEBINS=$(grep "^\* ZENBINS " "$RUNPAR" | sed -e 's/\* ZENBINS//' | sed -e 's/ /\n/g')
 fi
 echo "Zenith angle definition: $ZEBINS"
 declare -a ZEBINARRAY=( $ZEBINS ) #convert to array
diff --git a/scripts/IRF.trainXGBforAngularReconstructionBinned.sh b/scripts/IRF.trainXGBforAngularReconstructionBinned.sh
index 08025876..b28fbfae 100755
--- a/scripts/IRF.trainXGBforAngularReconstructionBinned.sh
+++ b/scripts/IRF.trainXGBforAngularReconstructionBinned.sh
@@ -73,7 +73,7 @@ MSCWLIST="$ODIR/xgbFiles.list"
 rm -f ${MSCWLIST}
 touch ${MSCWLIST}
 
-INDIR="$VERITAS_IRFPRODUCTION_DIR/$EDVERSION/${ANALYSIS_TYPE}/$SIMTYPE/${EPOCH}_ATM${ATM}_gamma/MSCW_RECID0_DISP"
+INDIR="$VERITAS_IRFPRODUCTION_DIR/$EDVERSION/${ANALYSIS_TYPE}/$SIMTYPE/${EPOCH}_ATM${ATM}_gamma/MSCW_RECID${RECID}_DISP"
 
 STEREO_PAR="$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/XGB-stereo-parameter.json"
 TRAIN_ANGLES=$(jq -r ".zenith[] | select(.id==\"$ZA\") | .train | join(\" \")" $STEREO_PAR)
diff --git a/scripts/db_scripts/db_combine_dqm_fits.py b/scripts/db_scripts/db_combine_dqm_fits.py
index aa899259..51f7b966 100755
--- a/scripts/db_scripts/db_combine_dqm_fits.py
+++ b/scripts/db_scripts/db_combine_dqm_fits.py
@@ -49,7 +49,7 @@ def combine_tables(file_list, output_file):
 
         combined_tables.extend(batch_tables)
 
-    final_combined_table = vstack(combined_tables, join_type="exact")
+    final_combined_table = vstack(combined_tables, join_type="outer")
     logging.info(f"Writing combined table to {output_file}")
     final_combined_table.write(output_file, overwrite=True)
 
diff --git a/scripts/db_scripts/db_run.sh b/scripts/db_scripts/db_run.sh
index 03164b87..e394419a 100755
--- a/scripts/db_scripts/db_run.sh
+++ b/scripts/db_scripts/db_run.sh
@@ -74,6 +74,7 @@ get_start_time()
     else
         field_name="data_start_time"
     fi
+    start_time_index=0
     while IFS="|" read -ra a; do
         if [[ ${a[0]} == "run_id" ]]; then
             for (( j=0; j<${#a[@]}; j++ ));
@@ -97,6 +98,7 @@ get_end_time()
     else
         field_name="data_end_time"
     fi
+    end_time_index=0
     while IFS="|" read -ra a; do
         if [[ ${a[0]} == "run_id" ]]; then
             for (( j=0; j<${#a[@]}; j++ ));
@@ -170,6 +172,7 @@ get_source_id()
     else
         OFIL=$(cat $OFIL)
     fi
+    source_index=0
     while IFS="|" read -ra a; do
         if [[ ${a[0]} == "run_id" ]]; then
             for (( j=0; j<${#a[@]}; j++ ));
@@ -289,9 +292,11 @@ read_pointing()
 
 read_run_from_DB runinfo
 read_run_from_DB rundqm
-# don't test and read if tar file exists
-# (implementation of testing missing)
-if [[ ! -e $(getDBTextFileDirectory ${RUN}).tar.gz ]] || [[ ${OVERWRITE} == "1" ]]; then
+# Re-read laser data if tarball is missing OR if sidecar .laserrun file is absent
+RUND="$(getDBTextFileDirectory ${RUN})"
+if [[ ! -e "${RUND}.tar.gz" ]] || \
+   [[ $(get_file_status ${RUN} "${RUND}/${RUN}.laserrun") == "0" ]] || \
+   [[ ${OVERWRITE} == "1" ]]; then
     read_laser_run_and_dqm
     read_laser_calibration
 fi
diff --git a/scripts/db_scripts/db_write_fits.py b/scripts/db_scripts/db_write_fits.py
index 51139e68..d57c23c8 100755
--- a/scripts/db_scripts/db_write_fits.py
+++ b/scripts/db_scripts/db_write_fits.py
@@ -106,7 +106,8 @@ def extract_l3_rate(run, temp_run_dir):
     table = table[condition]
     time_diffs = np.diff(np.array(table["timestamp"])) / 1000.0
     l3_values = np.diff(np.array(table["L3"], dtype=float))
-    l3_values /= time_diffs
+    with np.errstate(divide="ignore", invalid="ignore"):
+        l3_values = np.where(time_diffs > 0, l3_values / time_diffs, np.nan)
 
     if len(l3_values) > 0:
         l3_mean = np.mean(l3_values)
@@ -129,8 +130,10 @@ def extract_l3_rate(run, temp_run_dir):
         l3_busy = np.array(table["L3orVDAQBusyScaler"], dtype=float)
         busy = np.diff(l3_busy)
         ten_mhz = np.diff(np.array(table["TenMHzScaler"]))
-        dead_time = np.mean(busy / ten_mhz)
-        dead_time_std = np.std(busy / ten_mhz)
+        with np.errstate(divide="ignore", invalid="ignore"):
+            ratio = np.where(ten_mhz > 0, busy / ten_mhz, np.nan)
+        dead_time = np.mean(ratio)
+        dead_time_std = np.std(ratio)
     except ValueError:
         dead_time = np.nan
         dead_time_std = np.nan
@@ -426,9 +429,9 @@ def main():
             file_path = os.path.join(temp_run_files, file_name)
             logging.info("Converting %s", file_path)
             table = read_file(file_path)
-            if "dqm" in file_name.lower():
-                convert_table_comment_to_ascii(table)
             if table is not None:
+                if "dqm" in file_name.lower():
+                    convert_table_comment_to_ascii(table)
                 hdu.append(fits.BinTableHDU(table))
                 hdu[-1].name = file_name.split(".")[1]
 
diff --git a/scripts/helper_scripts/ANALYSIS.anasum_sub.sh b/scripts/helper_scripts/ANALYSIS.anasum_sub.sh
index eb60af6d..86ae2393 100755
--- a/scripts/helper_scripts/ANALYSIS.anasum_sub.sh
+++ b/scripts/helper_scripts/ANALYSIS.anasum_sub.sh
@@ -74,22 +74,6 @@ rm -f $OUTPUTLOGFILE
 touch $OUTPUTLOGFILE
 
 
-prepare_atmo_string()
-{
-    ATMO=$1
-    EPOCH=$2
-    OBSL=$3
-    # V4 and V5: grisu sims with ATM21/22
-    if [[ $EPOCH == *"V4"* ]] || [[ $EPOCH == *"V5"* ]]; then
-        ATMO=${ATMO/6/2}
-    fi
-    # V6 UV only for ATM 61
-    if [[ $EPOCH == *"V6"* ]] && [[ $OBSL == "obsFilter" ]]; then
-       ATMO=${ATMO/62/61}
-    fi
-    echo "$ATMO"
-}
-
 inspect_executables()
 {
     if [ -n "$EVNDISP_APPTAINER" ]; then
@@ -144,8 +128,6 @@ if [[ $FLIST == "NOTDEFINED" ]]; then
     OBSL=$(echo $RUNINFO | awk '{print $4}')
     TELTOANA=`echo $RUNINFO | awk '{print "T"$(5)}'`
 
-    ATMO=$(prepare_atmo_string $ATMO $EPOCH $OBSL)
-
     REPLACESIMTYPEEff=$(prepare_irf_string $EPOCH $OBSL $SIMTYPE 0)
     REPLACESIMTYPERad=$(prepare_irf_string $EPOCH $OBSL $SIMTYPE 1)
 
diff --git a/scripts/helper_scripts/ANALYSIS.evndisp_sub.sh b/scripts/helper_scripts/ANALYSIS.evndisp_sub.sh
index 0a0f6c57..da1d382e 100755
--- a/scripts/helper_scripts/ANALYSIS.evndisp_sub.sh
+++ b/scripts/helper_scripts/ANALYSIS.evndisp_sub.sh
@@ -74,11 +74,18 @@ unpack_db_textdirectory()
     echo "DBTEXT FILE for $RRUN $DBRUNFIL" >&2
     if [[ -e ${DBRUNFIL} ]]; then
         mkdir -p ${TMP_DBTEXTDIRECTORY}/${SRUN}
-        tar -xzf ${DBRUNFIL} -C ${TMP_DBTEXTDIRECTORY}/${SRUN}/
+        tar -xzf ${DBRUNFIL} -C ${TMP_DBTEXTDIRECTORY}/${SRUN}/ || return 1
     else
         echo "DBTEXT FILE not found ($DBRUNFIL)" >&2
+        return 1
     fi
-    echo "${TMP_DBTEXTDIRECTORY}/${SRUN}/${RRUN}/${RRUN}.laserrun"
+
+    DBTEXTFILE="${TMP_DBTEXTDIRECTORY}/${SRUN}/${RRUN}/${RRUN}.laserrun"
+    if [[ ! -r ${DBTEXTFILE} ]]; then
+        echo "DBTEXT FILE not readable (${DBTEXTFILE})" >&2
+        return 1
+    fi
+    echo "${DBTEXTFILE}"
 }
 
 sub_dir()
@@ -98,11 +105,15 @@ if [[ "${DBTEXTDIRECTORY}" != "0" ]]; then
     echo "UNPACKING DBTEXT from $RUN ${DBTEXTDIRECTORY}"
     TMP_DBTEXTDIRECTORY="${TEMPDIR}/DBTEXT"
     TMP_LASERRUN=$(unpack_db_textdirectory $RUN $TMP_DBTEXTDIRECTORY)
+    if [[ $? -ne 0 || ! -r ${TMP_LASERRUN} ]]; then
+        echo "failed to unpack DBTEXT laser-run metadata for run $RUN" >&2
+        exit 1
+    fi
     LRUNID=$(cat ${TMP_LASERRUN} | grep -v run_id | awk -F "|" '{print $1}')
     for LL in ${LRUNID}
     do
         echo "  unpacking flasher/laser run: $LL"
-        unpack_db_textdirectory $LL $TMP_DBTEXTDIRECTORY
+        unpack_db_textdirectory $LL $TMP_DBTEXTDIRECTORY >/dev/null || exit 1
     done
     echo "DBTEXT directory $(ls -l $TMP_DBTEXTDIRECTORY)"
 
@@ -136,6 +147,10 @@ get_run_date()
 # check if run is on disk
 if [[ "${DBTEXTDIRECTORY}" != "0" ]]; then
     RUNINFO=$(sub_dir ${TMP_DBTEXTDIRECTORY} ${RUN})/${RUN}/${RUN}.runinfo
+    if [[ ! -r ${RUNINFO} ]]; then
+        echo "DBTEXT run info not readable (${RUNINFO})" >&2
+        exit 1
+    fi
     RUNDATE=$(get_run_date ${RUNINFO})
     echo "RUN $RUN $RUNINFO $RUNDATE"
     ls -l ${TMP_DBTEXTDIRECTORY}
diff --git a/scripts/helper_scripts/ANALYSIS.mscw_energy_sub.sh b/scripts/helper_scripts/ANALYSIS.mscw_energy_sub.sh
index ab143ec3..4e3356ad 100755
--- a/scripts/helper_scripts/ANALYSIS.mscw_energy_sub.sh
+++ b/scripts/helper_scripts/ANALYSIS.mscw_energy_sub.sh
@@ -137,13 +137,13 @@ get_disp_dir()
     elif (( $(echo "$ZA < 58" | bc -l) )); then
         DISPDIR="${DISPDIR}/55deg/"
     elif (( $(echo "$ZA < 62" | bc -l) )); then
-        if [[ ${SIMTYPE_RUN} == "CARE_RedHV" ]]; then  # fix for incomplete MC set
+        if [[ ${HVSETTINGS} == "obsLowHV" ]]; then  # fix for incomplete RedHV MC set
             DISPDIR="${DISPDIR}/55deg/"
         else
             DISPDIR="${DISPDIR}/60deg/"
         fi
     else
-        if [[ ${SIMTYPE_RUN} == "CARE_RedHV" ]]; then  # fix for incomplete MC set
+        if [[ ${HVSETTINGS} == "obsLowHV" ]]; then  # fix for incomplete RedHV MC set
             DISPDIR="${DISPDIR}/55deg/"
         else
             DISPDIR="${DISPDIR}/60deg/"
@@ -156,6 +156,10 @@ if [[ $DISPBDT == "1" ]]; then
     ZA=$($EVNDISPSYS/bin/printRunParameter $INFILEPATH -zenith | awk '{print $4}')
     DISPDIR=$(get_disp_dir ${ZA})
     echo "DISPDIR (Zenith is $ZA deg): " $DISPDIR
+    if [[ ! -d "$DISPDIR" ]]; then
+        echo "Error: DispBDT directory $DISPDIR not found, exiting..."
+        exit 1
+    fi
 fi
 
 #################################
@@ -206,7 +210,7 @@ $EVNDISPSYS/bin/mscw_energy         \
 echo "$(inspect_executables)" >> ${MSCWLOGFILE}
 
 # write DISP directory into log file (as tmp directories are used)
-if [[ DISPBDT != "NOTSET" ]]; then
+if [[ $DISPBDT != "NOTSET" ]]; then
     echo "" >> ${MSCWLOGFILE}
     echo "dispBDT XML files read from ${DISPDIR}" >> ${MSCWLOGFILE}
 fi
diff --git a/scripts/helper_scripts/ANALYSIS.v2dl3_sub.sh b/scripts/helper_scripts/ANALYSIS.v2dl3_sub.sh
index c99db244..3333ac48 100755
--- a/scripts/helper_scripts/ANALYSIS.v2dl3_sub.sh
+++ b/scripts/helper_scripts/ANALYSIS.v2dl3_sub.sh
@@ -55,7 +55,8 @@ check_conda_installation
 
 source activate base
 conda activate v2dl3Eventdisplay-${V2DL3VERSION}
-pip install -e "${V2DL3SYS%/}-v${V2DL3VERSION}"
+# Install only if not already present (avoid slow per-job reinstall)
+pip show v2dl3-eventdisplay &>/dev/null 2>&1 || pip install -e "${V2DL3SYS%/}-v${V2DL3VERSION}"
 
 V2DL3OPT="--fuzzy_boundary zenith 0.05 --fuzzy_boundary pedvar 0.5 --save_multiplicity"
 # selection for full-gamma files
diff --git a/scripts/helper_scripts/IRF.compress_evndisp_MC_sub.sh b/scripts/helper_scripts/IRF.compress_evndisp_MC_sub.sh
index 0f7f833b..c2003a96 100755
--- a/scripts/helper_scripts/IRF.compress_evndisp_MC_sub.sh
+++ b/scripts/helper_scripts/IRF.compress_evndisp_MC_sub.sh
@@ -45,7 +45,7 @@ add_log_file()
 
 compress_file()
 {
-    if command -v zstd /dev/null; then
+    if command -v zstd &>/dev/null; then
         zstd ${1}
         zstd --test ${1}.zst
     else
diff --git a/scripts/helper_scripts/IRF.evndisp_MC_sub.sh b/scripts/helper_scripts/IRF.evndisp_MC_sub.sh
index 07a2fc3e..400ef5b5 100755
--- a/scripts/helper_scripts/IRF.evndisp_MC_sub.sh
+++ b/scripts/helper_scripts/IRF.evndisp_MC_sub.sh
@@ -91,6 +91,7 @@ if [ -e "$V4N" ]; then
     mkdir -p "$TMPDIR"
     VBF_BASENAME="${VBFNAME%.zst}"
     echo "Checking processed files in $V4N"
+    shopt -s nullglob
     for file in "$V4N"/*.root.zst; do
         tmpfile="$TMPDIR/$(basename "${file%.zst}")"
         zstd -d -c "$file" > "$tmpfile"
@@ -99,6 +100,7 @@ if [ -e "$V4N" ]; then
             exit
         fi
     done
+    shopt -u nullglob
     rm -rf "$TMPDIR"
 fi
 
@@ -322,7 +324,7 @@ compare_log_file evndisptzeroLog $ODIR/$ONAME.tzero.log
 ### compress evndisp root file
 compress_file()
 {
-    if command -v zstd /dev/null; then
+    if command -v zstd &>/dev/null; then
         zstd ${1}
         zstd --test ${1}.zst
     else
diff --git a/scripts/helper_scripts/IRF.lookup_table_parallel_sub.sh b/scripts/helper_scripts/IRF.lookup_table_parallel_sub.sh
index b51ec7bb..868bb810 100755
--- a/scripts/helper_scripts/IRF.lookup_table_parallel_sub.sh
+++ b/scripts/helper_scripts/IRF.lookup_table_parallel_sub.sh
@@ -64,7 +64,7 @@ if [ -n "$(find ${INDIR} -name "*[0-9].root" 2>/dev/null)" ]; then
     echo "Copying evndisp root files to ${DDIR}"
     find ${INDIR} -name "*[0-9].root" -exec cp -v {} ${DDIR} \;
 elif [ -n "$(find  ${INDIR} -name "*[0-9].root.zst" 2>/dev/null)" ]; then
-    if command -v zstd /dev/null; then
+    if command -v zstd &>/dev/null; then
         echo "Copying evndisp root.zst files to ${DDIR}"
         FLIST=$(find "${INDIR}/" -name "*[0-9].root.zst")
         for F in $FLIST
diff --git a/scripts/helper_scripts/IRF.mscw_energy_MC_sub.sh b/scripts/helper_scripts/IRF.mscw_energy_MC_sub.sh
index 3fd4d167..63873312 100755
--- a/scripts/helper_scripts/IRF.mscw_energy_MC_sub.sh
+++ b/scripts/helper_scripts/IRF.mscw_energy_MC_sub.sh
@@ -73,7 +73,6 @@ inspect_executables()
     fi
 }
 
-
 # mscw_energy command line options
 MOPT="-noNoTrigger -nomctree -writeReconstructedEventsOnly=1 -arrayrecid=${RECID} -tablefile $TABFILE"
 # dispBDT reconstruction
@@ -104,14 +103,16 @@ if [ $DISPBDT -eq 1 ]; then
     elif [[ "${ZA}" -lt "58" ]]; then
         DISPDIR="${DISPDIR}/55deg/"
     elif [[ "${ZA}" -lt "62" ]]; then
-        DISPDIR="${DISPDIR}/60deg/"
-        if [[ ${SIMTYPE} == "CARE_RedHV" ]]; then  # fix for incomplete MC set
+        if [[ ${SIMTYPE} == CARE_RedHV* ]]; then  # fix for incomplete RedHV MC set
             DISPDIR="${DISPDIR}/55deg/"
+        else
+            DISPDIR="${DISPDIR}/60deg/"
         fi
     else
-        DISPDIR="${DISPDIR}/65deg/"
-        if [[ ${SIMTYPE} == "CARE_RedHV" ]]; then  # fix for incomplete MC set
+        if [[ ${SIMTYPE} == CARE_RedHV* ]]; then  # fix for incomplete RedHV MC set
             DISPDIR="${DISPDIR}/55deg/"
+        else
+            DISPDIR="${DISPDIR}/65deg/"
         fi
     fi
     # unzip XML files into DDIR
@@ -130,11 +131,11 @@ fi
 rm -f $OSUBDIR/$OFILE.log
 rm -f $OSUBDIR/$OFILE.list
 echo "INDIR ${INDIR}"
-if [ -n "$(find "${INDIR}/" -name "*[0-9].root" 2>/dev/null)" ]; then
+if [ -n "$(find "${INDIR}/" -maxdepth 1 -name "*[0-9].root" 2>/dev/null)" ]; then
     echo "Using evndisp root files from ${INDIR}"
-    cp -v "${INDIR}/*[0-9].root" "$DDIR"
+    find "${INDIR}/" -maxdepth 1 -name "*[0-9].root" -exec cp -v {} "$DDIR" \;
 elif [ -n "$(find  "${INDIR}/" -name "*[0-9].root.zst" 2>/dev/null)" ]; then
-    if command -v zstd /dev/null; then
+    if command -v zstd &>/dev/null; then
         echo "Copying evndisp root.zst files to ${DDIR}"
         FLIST=$(find "${INDIR}/" -name "*[0-9].root.zst")
         for F in $FLIST
diff --git a/scripts/helper_scripts/IRF.optimizeTMVAforGammaHadronSeparation_sub.sh b/scripts/helper_scripts/IRF.optimizeTMVAforGammaHadronSeparation_sub.sh
index 2892d54c..6c0e1ec7 100755
--- a/scripts/helper_scripts/IRF.optimizeTMVAforGammaHadronSeparation_sub.sh
+++ b/scripts/helper_scripts/IRF.optimizeTMVAforGammaHadronSeparation_sub.sh
@@ -54,7 +54,6 @@ then
     rm -f ${RATEFILE}.log
 
     # calculate rates from Crab Nebula and from background rates
-    rm -f ${MVADIR}/rates.log
     "$EVNDISPSYS"/bin/calculateCrabRateFromMC \
         ${EFFAREA} \
         ${RATEFILE}.root \
diff --git a/scripts/helper_scripts/IRF.trainXGBforAngularReconstruction_sub.sh b/scripts/helper_scripts/IRF.trainXGBforAngularReconstruction_sub.sh
index e6afb030..74c218da 100755
--- a/scripts/helper_scripts/IRF.trainXGBforAngularReconstruction_sub.sh
+++ b/scripts/helper_scripts/IRF.trainXGBforAngularReconstruction_sub.sh
@@ -13,8 +13,8 @@ N="5000000"
 MAXCORES=48
 
 # temporary (scratch) directory
-if [[ -n $TMPDIR ]]; then
-    TEMPDIR=$TMPDIR/$(basename $MSCW_FILE .root)
+if [[ -n "$TMPDIR" ]]; then
+    TEMPDIR="${TMPDIR}/XGB-$(basename "$LLIST" .list)-$(uuidgen)"
 else
     TEMPDIR="$VERITAS_USER_DATA_DIR/TMPDIR"
 fi
diff --git a/scripts/set_environment.sh b/scripts/set_environment.sh
index 006b3e41..5b1b333b 100755
--- a/scripts/set_environment.sh
+++ b/scripts/set_environment.sh
@@ -61,7 +61,7 @@ export V2DL3SYS=${USERAFSDIR}/EVNDISP/EVNDISP-400/GITHUB_Eventdisplay/PreProcess
 export EVNDISP_MLSYS=${USERAFSDIR}/EVNDISP/EVNDISP-400/GITHUB_Eventdisplay/Eventdisplay-ML
 # EVENTDISPLAY using apptainers
 if [[ $PROCESS == "apptainer"* ]]; then
-    export EVNDISP_APPTAINER="$VERITAS_DATA_DIR/shared/APPTAINERS/eventdisplay_v4_${EVNDISPVERSION}-rc3.sif"
+    export EVNDISP_APPTAINER="$VERITAS_DATA_DIR/shared/APPTAINERS/eventdisplay_v4_${EVNDISPVERSION}-rc4.sif"
     export EVNDISP_ENV="--env VERITAS_DATA_DIR=${VERITAS_DATA_DIR},VERITAS_EVNDISP_AUX_DIR=${VERITAS_EVNDISP_AUX_DIR},VERITAS_USER_DATA_DIR=${VERITAS_USER_DATA_DIR},VERITAS_USER_LOG_DIR=${VERITAS_USER_LOG_DIR}"
     export EVNDISPSYS="apptainer exec --no-mount bind-paths --cleanenv ${EVNDISP_APPTAINER} /opt/EventDisplay_v4/"
     # Alma Linux 9 (al9) processing