diff --git a/jobs/JGDAS_ATMOS_ANALYSIS_DIAG b/jobs/JGDAS_ATMOS_ANALYSIS_DIAG
index 2733c30ce6b..70013e5e1af 100755
--- a/jobs/JGDAS_ATMOS_ANALYSIS_DIAG
+++ b/jobs/JGDAS_ATMOS_ANALYSIS_DIAG
@@ -32,12 +32,9 @@ mkdir -m 775 -p "${COMOUT_ATMOS_ANALYSIS}"
 
 ###############################################################
 # Run relevant script
-${ANALDIAGSH:-${SCRgfs}/exglobal_diag.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${ANALDIAGSH:-${SCRgfs}/exglobal_diag.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # End JOB SPECIFIC work
diff --git a/jobs/JGDAS_ATMOS_CHGRES_FORENKF b/jobs/JGDAS_ATMOS_CHGRES_FORENKF
index d2f7012cf8e..61b99d12816 100755
--- a/jobs/JGDAS_ATMOS_CHGRES_FORENKF
+++ b/jobs/JGDAS_ATMOS_CHGRES_FORENKF
@@ -25,12 +25,9 @@ MEMDIR="mem001" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
 
 ###############################################################
 # Run relevant script
-${CHGRESFCSTSH:-${SCRgfs}/exgdas_atmos_chgres_forenkf.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${CHGRESFCSTSH:-${SCRgfs}/exgdas_atmos_chgres_forenkf.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # End JOB SPECIFIC work
diff --git a/jobs/JGDAS_ATMOS_VERFOZN b/jobs/JGDAS_ATMOS_VERFOZN
index 0a9b92eaefe..87bb29e4b43 100755
--- a/jobs/JGDAS_ATMOS_VERFOZN
+++ b/jobs/JGDAS_ATMOS_VERFOZN
@@ -29,12 +29,9 @@ if [[ ! -d ${TANKverf_ozn} ]]; then mkdir -p ${TANKverf_ozn} ; fi
 #-------------------------------------------------------
 # Execute the script.
 #
-"${SCRgfs}/exgdas_atmos_verfozn.sh"
-err=$?
-if (( err != 0 )); then
-    exit "${err}"
-fi
-
+"${SCRgfs}/exgdas_atmos_verfozn.sh" && true
+export err=$?
+err_chk
 
 ################################
 # Remove the Working Directory
diff --git a/jobs/JGDAS_ATMOS_VERFRAD b/jobs/JGDAS_ATMOS_VERFRAD
index ac18460a193..43faa5cae87 100755
--- a/jobs/JGDAS_ATMOS_VERFRAD
+++ b/jobs/JGDAS_ATMOS_VERFRAD
@@ -33,11 +33,9 @@ if [[ ! -d ${TANKverf_rad} ]]; then mkdir -p ${TANKverf_rad} ; fi
 
 ########################################################
 # Execute the script.
-"${SCRgfs}/exgdas_atmos_verfrad.sh"
-err=$?
-if (( err != 0 )); then
-    exit "${err}"
-fi
+"${SCRgfs}/exgdas_atmos_verfrad.sh" && true
+export err=$?
+err_chk
 
 ################################
 # Remove the Working Directory
diff --git a/jobs/JGDAS_ENKF_DIAG b/jobs/JGDAS_ENKF_DIAG
index aa3eb1ddfea..1c2bf151fe7 100755
--- a/jobs/JGDAS_ENKF_DIAG
+++ b/jobs/JGDAS_ENKF_DIAG
@@ -44,8 +44,8 @@ MEMDIR="ensstat" RUN=${GDUMP_ENS} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
 
 export ATMGES_ENSMEAN="${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf006.ensmean.nc"
 if [ ! -f ${ATMGES_ENSMEAN} ]; then
-    echo "FATAL ERROR: FILE MISSING: ATMGES_ENSMEAN = ${ATMGES_ENSMEAN}"
-    exit 1
+    export err=1
+    err_chk "FATAL ERROR: FILE MISSING: ATMGES_ENSMEAN = ${ATMGES_ENSMEAN}"
 fi
 
 # Link observational data
@@ -99,12 +99,9 @@ done
 ###############################################################
 # Run relevant script
 
-${ANALDIAGSH:-${SCRgfs}/exglobal_diag.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${ANALDIAGSH:-${SCRgfs}/exglobal_diag.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # End JOB SPECIFIC work
diff --git a/jobs/JGDAS_ENKF_ECEN b/jobs/JGDAS_ENKF_ECEN
index b3f5c03203b..57c676ad813 100755
--- a/jobs/JGDAS_ENKF_ECEN
+++ b/jobs/JGDAS_ENKF_ECEN
@@ -40,12 +40,9 @@ MEMDIR="ensstat" RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
 ###############################################################
 # Run relevant script
 
-${ENKFRECENSH:-${SCRgfs}/exgdas_enkf_ecen.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${ENKFRECENSH:-${SCRgfs}/exgdas_enkf_ecen.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # End JOB SPECIFIC work
diff --git a/jobs/JGDAS_ENKF_POST b/jobs/JGDAS_ENKF_POST
index 244566ac5b3..0cf3dc0d1dc 100755
--- a/jobs/JGDAS_ENKF_POST
+++ b/jobs/JGDAS_ENKF_POST
@@ -21,12 +21,9 @@ export LEVS=$((LEVS-1))
 ###############################################################
 # Run relevant script
 
-${ENKFPOSTSH:-${SCRgfs}/exgdas_enkf_post.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${ENKFPOSTSH:-${SCRgfs}/exgdas_enkf_post.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # End JOB SPECIFIC work
diff --git a/jobs/JGDAS_ENKF_SELECT_OBS b/jobs/JGDAS_ENKF_SELECT_OBS
index aa82d53eae5..f354991bbf6 100755
--- a/jobs/JGDAS_ENKF_SELECT_OBS
+++ b/jobs/JGDAS_ENKF_SELECT_OBS
@@ -51,18 +51,14 @@ mkdir -p "${COMOUT_ATMOS_ANALYSIS}"
 
 export ATMGES_ENSMEAN="${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf006${GSUFFIX}"
 if [[ ! -f ${ATMGES_ENSMEAN} ]]; then
-    echo "FATAL ERROR: FILE MISSING: ATMGES_ENSMEAN = ${ATMGES_ENSMEAN}"
-    exit 1
+    export err=1
+    err_chk "FATAL ERROR: FILE MISSING: ATMGES_ENSMEAN = ${ATMGES_ENSMEAN}"
 fi
 
-# Ignore masking of chained commands and possible misspelling warning
-# shellcheck disable=SC2153,SC2312
-LEVS=$(${NCDUMP} -h "${ATMGES_ENSMEAN}" | grep -i "pfull" | head -1 | awk -F" = " '{print $2}' | awk -F" " '{print $1}') # get LEVS
-# shellcheck disable=
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
+LEVS=$(${NCLEN} ${ATMGES} pfull) && true
+export err=$?
+set_strict
+
 export LEVS
 
 # Link observational data
@@ -121,12 +117,9 @@ done
 ###############################################################
 # Run relevant script
 
-${INVOBSSH:-${SCRgfs}/exgdas_enkf_select_obs.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${INVOBSSH:-${SCRgfs}/exgdas_enkf_select_obs.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # Send Alerts
@@ -144,7 +137,7 @@ fi
 # Final processing
 ##############################################
 if [[ -e "${pgmout}" ]] ; then
-  cat ${pgmout}
+  cat "${pgmout}"
 fi
 
 ##########################################
diff --git a/jobs/JGDAS_ENKF_SFC b/jobs/JGDAS_ENKF_SFC
index f0ddc93429e..a81453b8f90 100755
--- a/jobs/JGDAS_ENKF_SFC
+++ b/jobs/JGDAS_ENKF_SFC
@@ -42,12 +42,9 @@ RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
 ###############################################################
 # Run relevant script
 
-${ENKFRESFCSH:-${SCRgfs}/exgdas_enkf_sfc.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${ENKFRESFCSH:-${SCRgfs}/exgdas_enkf_sfc.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # End JOB SPECIFIC work
diff --git a/jobs/JGDAS_ENKF_UPDATE b/jobs/JGDAS_ENKF_UPDATE
index 24faf5469fb..56a0260e1a9 100755
--- a/jobs/JGDAS_ENKF_UPDATE
+++ b/jobs/JGDAS_ENKF_UPDATE
@@ -36,12 +36,9 @@ MEMDIR="ensstat" RUN="enkfgdas" YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
 ###############################################################
 # Run relevant script
 
-${ENKFUPDSH:-${SCRgfs}/exgdas_enkf_update.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${ENKFUPDSH:-${SCRgfs}/exgdas_enkf_update.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # Send Alerts
diff --git a/jobs/JGLOBAL_ARCHIVE_TARS b/jobs/JGLOBAL_ARCHIVE_TARS
index 87127b94172..0d53480a5b6 100755
--- a/jobs/JGLOBAL_ARCHIVE_TARS
+++ b/jobs/JGLOBAL_ARCHIVE_TARS
@@ -75,7 +75,10 @@ fi
 
 set +eu
 ${GLOBALARCHIVESH:-${SCRgfs}/exglobal_archive_tars.py}
-export err=$?; err_chk "FATAL ERROR: failed to archive the COM structure"
+export err=$?
+set +x
+err_chk "FATAL ERROR: failed to archive the COM structure"
+set_trace
 set_strict
 
 ##############################################
diff --git a/jobs/JGLOBAL_ATMOS_ANALYSIS b/jobs/JGLOBAL_ATMOS_ANALYSIS
index e015ae131f8..8d9212dd805 100755
--- a/jobs/JGLOBAL_ATMOS_ANALYSIS
+++ b/jobs/JGLOBAL_ATMOS_ANALYSIS
@@ -45,23 +45,20 @@ mkdir -p "${COMOUT_ATMOS_ANALYSIS}"
 
 export ATMGES="${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf006.nc"
 if [ ! -f ${ATMGES} ]; then
-    echo "FATAL ERROR: FILE MISSING: ATMGES = ${ATMGES}"
-    exit 1
+    export err=1
+    err_chk "FATAL ERROR: FILE MISSING: ATMGES = ${ATMGES}"
 fi
 
 # Get LEVS
-export LEVS=$(${NCLEN} ${ATMGES} pfull)
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+export LEVS=$(${NCLEN} ${ATMGES} pfull) && true
+export err=$?
+err_chk
 
 if [ ${DOHYBVAR} = "YES" ]; then
     export ATMGES_ENSMEAN="${COMIN_ATMOS_HISTORY_ENS_PREV}/${GPREFIX_ENS}atmf006.ensmean.nc"
     if [ ! -f ${ATMGES_ENSMEAN} ]; then
-        echo "FATAL ERROR: FILE MISSING: ATMGES_ENSMEAN = ${ATMGES_ENSMEAN}"
-        exit 2
+        export err=2
+        err_chk "FATAL ERROR: FILE MISSING: ATMGES_ENSMEAN = ${ATMGES_ENSMEAN}"
     fi
 fi
 
@@ -89,12 +86,9 @@ fi
 ###############################################################
 # Run relevant script
 
-${ANALYSISSH:-${SCRgfs}/exglobal_atmos_analysis.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${ANALYSISSH:-${SCRgfs}/exglobal_atmos_analysis.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # Send Alerts
diff --git a/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC b/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC
index 255e29774a4..d72c4ecc92b 100755
--- a/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC
+++ b/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC
@@ -41,17 +41,14 @@ RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
 
 export ATMGES="${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf006.nc"
 if [ ! -f ${ATMGES} ]; then
-    echo "FATAL ERROR: FILE MISSING: ATMGES = ${ATMGES}"
-    exit 1
+    export err=1
+    err_chk "FATAL ERROR: FILE MISSING: ATMGES = ${ATMGES}"
 fi
 
 # Get LEVS
-export LEVS=$(${NCLEN} ${ATMGES} pfull)
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+export LEVS=$(${NCLEN} ${ATMGES} pfull) && true
+export err=$?
+err_chk
 
 # Generate Gaussian surface analysis  # TODO: Should this be removed now that sfcanl is its own job?
 export DOGAUSFCANL=${DOGAUSFCANL:-"YES"}
@@ -60,12 +57,9 @@ export DOGAUSFCANL=${DOGAUSFCANL:-"YES"}
 ###############################################################
 # Run relevant script
 
-${ANALCALCSH:-${SCRgfs}/exglobal_atmos_analysis_calc.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${ANALCALCSH:-${SCRgfs}/exglobal_atmos_analysis_calc.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # End JOB SPECIFIC work
diff --git a/jobs/JGLOBAL_ATMOS_SFCANL b/jobs/JGLOBAL_ATMOS_SFCANL
index 33a5150040c..233f4e2f99c 100755
--- a/jobs/JGLOBAL_ATMOS_SFCANL
+++ b/jobs/JGLOBAL_ATMOS_SFCANL
@@ -32,12 +32,9 @@ mkdir -p "${COMOUT_ATMOS_RESTART}"
 ###############################################################
 # Run relevant script
 
-${SFCANALSH:-${SCRgfs}/exglobal_atmos_sfcanl.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${SFCANALSH:-${SCRgfs}/exglobal_atmos_sfcanl.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # End JOB SPECIFIC work
diff --git a/jobs/JGLOBAL_ATMOS_VMINMON b/jobs/JGLOBAL_ATMOS_VMINMON
index 84e1014c196..da82aae2962 100755
--- a/jobs/JGLOBAL_ATMOS_VMINMON
+++ b/jobs/JGLOBAL_ATMOS_VMINMON
@@ -31,11 +31,9 @@ if [[ ! -d ${M_TANKverf} ]]; then mkdir -p "${M_TANKverf}" ; fi
 
 ########################################################
 # Execute the script.
-"${SCRgfs}/exglobal_atmos_vminmon.sh"
-err=$?
-if (( err != 0 )); then
-    exit "${err}"
-fi
+"${SCRgfs}/exglobal_atmos_vminmon.sh" && true
+export err=$?
+err_chk
 
 ################################
 # Remove the Working Directory
diff --git a/jobs/JGLOBAL_ENS_ARCHIVE_TARS b/jobs/JGLOBAL_ENS_ARCHIVE_TARS
index dcb4d05210b..a57d405c5a1 100755
--- a/jobs/JGLOBAL_ENS_ARCHIVE_TARS
+++ b/jobs/JGLOBAL_ENS_ARCHIVE_TARS
@@ -21,7 +21,10 @@ if [[ ! -d ${COMOUT_CONF} ]]; then mkdir -p "${COMOUT_CONF}"; fi
 # Calls an external bash command; do not fail on unassigned/error
 set +eu
 "${SCRgfs}/exgdas_enkf_earc_tars.py"
-export err=$?; err_chk "FATAL ERROR Failed to archive the ensemble COM structure"
+export err=$?
+set +x
+err_chk "FATAL ERROR Failed to archive the ensemble COM structure"
+set_trace
 set_strict
 
 ###############################################################
diff --git a/scripts/exgdas_atmos_chgres_forenkf.sh b/scripts/exgdas_atmos_chgres_forenkf.sh
index 4794c5568b8..6e4bc79713c 100755
--- a/scripts/exgdas_atmos_chgres_forenkf.sh
+++ b/scripts/exgdas_atmos_chgres_forenkf.sh
@@ -154,8 +154,9 @@ EOF
          export pgm=$CHGRESNCEXEC
          . prep_step
 
-         $APRUN_CHGRES $CHGRESNCEXEC chgres_nc_gauss0$FHR.nml
-         export err=$?; err_chk
+         ${APRUN_CHGRES} "${CHGRESNCEXEC}" "chgres_nc_gauss0${FHR}.nml" && true
+         export err=$?
+         err_chk
      fi
    done
 
@@ -169,8 +170,9 @@ EOF
          export pgm=$CHGRESNCEXEC
          . prep_step
 
-         $APRUNCFP_CHGRES $DATA/mp_chgres.sh
-         export err=$?; err_chk
+         ${APRUNCFP_CHGRES} "${DATA}/mp_chgres.sh" && true
+         export err=$?
+         err_chk
       fi
    fi
 
diff --git a/scripts/exgdas_atmos_verfozn.sh b/scripts/exgdas_atmos_verfozn.sh
index 75d6ef973e0..0928569614d 100755
--- a/scripts/exgdas_atmos_verfozn.sh
+++ b/scripts/exgdas_atmos_verfozn.sh
@@ -7,7 +7,7 @@
 # (OznMon) DA package.
 #
 ################################################################################
-err=0
+export err=0
 
 data_available=0
 
@@ -36,13 +36,13 @@ if [[ -s ${oznstat} ]]; then
 
    export OZNMON_NETCDF=${netcdf}
 
-   "${USHgfs}/ozn_xtrct.sh"
-   err=$?
+   "${USHgfs}/ozn_xtrct.sh" && true
+   export err=$?
 
 else
    # oznstat file not found
-   err=1
+   export err=1
 fi
 
-exit ${err}
-
+err_chk
+exit 0
diff --git a/scripts/exgdas_atmos_verfrad.sh b/scripts/exgdas_atmos_verfrad.sh
index 8b8bb592b87..d429d7444da 100755
--- a/scripts/exgdas_atmos_verfrad.sh
+++ b/scripts/exgdas_atmos_verfrad.sh
@@ -19,6 +19,9 @@
 
 data_available=0
 
+# Do not exit on errors so that restricted data can be protected
+set +eu
+
 if [[ -s ${radstat} && -s ${biascr} ]]; then
    data_available=1
 
@@ -136,19 +139,13 @@ fi
 #####################################################################
 # Postprocessing
 
-err=0
+export err=0
 if [[ ${data_available} -ne 1 ]]; then
-   err=1
-elif [[ ${rc_angle} -ne 0 ]]; then
-   err=${rc_angle}
-elif [[ ${rc_bcoef} -ne 0 ]]; then
-   err=${rc_bcoef}
-elif [[ ${rc_bcor} -ne 0 ]]; then
-   err=${rc_bcor}
-elif [[ ${rc_time} -ne 0 ]]; then
-   err=${rc_time}
+   export err=1
 fi
 
+export err=$((err + rc_angle + rc_bcoef + rc_bcor + rc_time))
+
 #####################################################################
 # Restrict select sensors and satellites
 export CHGRP_CMD=${CHGRP_CMD:-"chgrp ${group_name:-rstprod}"}
@@ -159,5 +156,6 @@ for rtype in ${rlist}; do
   fi
 done
 
-exit ${err}
+err_chk
+exit "${err}"
 
diff --git a/scripts/exgdas_enkf_ecen.sh b/scripts/exgdas_enkf_ecen.sh
index d662bee61e1..ce8a76ada44 100755
--- a/scripts/exgdas_enkf_ecen.sh
+++ b/scripts/exgdas_enkf_ecen.sh
@@ -222,8 +222,13 @@ else
    LEVS_ENKF=${LEVS_ENKF:-$($NCLEN atminc_ensmean lev)} # get LEVS
 fi
 JCAP_ENKF=${JCAP_ENKF:--9999} # there is no jcap in these files
-[ $JCAP_ENKF -eq -9999 -a $LATB_ENKF -ne -9999 ] && JCAP_ENKF=$((LATB_ENKF-2))
-[ $LONB_ENKF -eq -9999 -o $LATB_ENKF -eq -9999 -o $LEVS_ENKF -eq -9999 -o $JCAP_ENKF -eq -9999 ] && exit -9999
+if [[ ${JCAP_ENKF} -eq -9999 && ${LATB_ENKF} -ne -9999 ]]; then
+   JCAP_ENKF=$((LATB_ENKF-2))
+fi
+if [[ ${LONB_ENKF} -eq -9999 || ${LATB_ENKF} -eq -9999 || ${LEVS_ENKF} -eq -9999 || ${JCAP_ENKF} -eq -9999 ]]; then
+   export err=9
+   err_chk
+fi
 
 ################################################################################
 # This is to give the user the option to recenter, default is YES
diff --git a/scripts/exgdas_enkf_post.sh b/scripts/exgdas_enkf_post.sh
index 9391608cba5..b388ebd2254 100755
--- a/scripts/exgdas_enkf_post.sh
+++ b/scripts/exgdas_enkf_post.sh
@@ -109,20 +109,20 @@ rc=0
 for fhr in $(seq $FHMIN $FHOUT $FHMAX); do
    fhrchar=$(printf %03i $fhr)
 
-   export pgm=$GETSFCENSMEANEXEC
+   export pgm=${GETSFCENSMEANEXEC}
    . prep_step
 
-   $APRUN_EPOS ${DATA}/$(basename $GETSFCENSMEANEXEC) ./ sfcf${fhrchar}.ensmean sfcf${fhrchar} $NMEM_ENS
+   ${APRUN_EPOS} "${DATA}/$(basename ${GETSFCENSMEANEXEC})" ./ "sfcf${fhrchar}.ensmean" "sfcf${fhrchar}" "${NMEM_ENS}" && true
    ra=$?
    rc=$((rc+ra))
 
-   export_pgm=$GETATMENSMEANEXEC
+   export pgm=${GETATMENSMEANEXEC}
    . prep_step
 
    if [ $ENKF_SPREAD = "YES" ]; then
-      $APRUN_EPOS ${DATA}/$(basename $GETATMENSMEANEXEC) ./ atmf${fhrchar}.ensmean atmf${fhrchar} $NMEM_ENS atmf${fhrchar}.ensspread
+      ${APRUN_EPOS} "${DATA}/$(basename ${GETATMENSMEANEXEC})" ./ "atmf${fhrchar}.ensmean" "atmf${fhrchar}" "${NMEM_ENS}" "atmf${fhrchar}.ensspread" && true
    else
-      $APRUN_EPOS ${DATA}/$(basename $GETATMENSMEANEXEC) ./ atmf${fhrchar}.ensmean atmf${fhrchar} $NMEM_ENS
+      ${APRUN_EPOS} "${DATA}/$(basename ${GETATMENSMEANEXEC})" ./ "atmf${fhrchar}.ensmean" "atmf${fhrchar}" "${NMEM_ENS}" && true
    fi
    ra=$?
    rc=$((rc+ra))
@@ -163,4 +163,4 @@ fi
 #  Postprocessing
 cd $pwd
 
-exit $err
+exit "${err}"
diff --git a/scripts/exgdas_enkf_sfc.sh b/scripts/exgdas_enkf_sfc.sh
index aeb3b24fb8b..9ced48bffc9 100755
--- a/scripts/exgdas_enkf_sfc.sh
+++ b/scripts/exgdas_enkf_sfc.sh
@@ -200,7 +200,7 @@ if [ $DOIAU = "YES" ]; then
 
         done # ensembles
 
-        CDATE="${PDY}${cyc}" ${CYCLESH}
+        CDATE="${PDY}${cyc}" "${CYCLESH}" && true
         export err=$?; err_chk
 
         # Copy outputs from DATA to COMOUT
@@ -271,7 +271,7 @@ if [[ "${DOSFCANL_ENKF}" == "YES" ]]; then
             fi
         done
 
-        CDATE="${PDY}${cyc}" ${CYCLESH}
+        CDATE="${PDY}${cyc}" "${CYCLESH}" && true
         export err=$?; err_chk
 
         # Copy outputs from DATA to COMOUT
diff --git a/scripts/exgdas_enkf_update.sh b/scripts/exgdas_enkf_update.sh
index 8073692fa45..670bb92338c 100755
--- a/scripts/exgdas_enkf_update.sh
+++ b/scripts/exgdas_enkf_update.sh
@@ -259,7 +259,7 @@ if [[ $USE_CFP = "YES" ]]; then
    if [[ $ncmd -gt 0 ]]; then
       ncmd_max=$((ncmd < max_tasks_per_node ? ncmd : max_tasks_per_node))
       APRUNCFP=$(eval echo $APRUNCFP)
-      $APRUNCFP $DATA/mp_untar.sh
+      ${APRUNCFP} "${DATA}/mp_untar.sh" && true
       export err=$?; err_chk
    fi
 fi
@@ -405,8 +405,9 @@ export pgm=$ENKFEXEC
 . prep_step
 
 $NCP $ENKFEXEC $DATA
-$APRUN_ENKF ${DATA}/$(basename $ENKFEXEC) 1>stdout 2>stderr
-export err=$?; err_chk
+$APRUN_ENKF "${DATA}/$(basename $ENKFEXEC)" 1>stdout 2>stderr && true
+export err=$?
+err_chk
 
 # Cat runtime output files.
 cat stdout stderr > "${COMOUT_ATMOS_ANALYSIS_STAT}/${ENKFSTAT}"
@@ -419,4 +420,4 @@ if [[ "${mkdata}" == "YES" ]]; then
 fi
 
 
-exit ${err}
+exit "${err}"
diff --git a/ush/jjob_header.sh b/ush/jjob_header.sh
index 3c5f85adc80..5efdc8fba1c 100755
--- a/ush/jjob_header.sh
+++ b/ush/jjob_header.sh
@@ -105,7 +105,9 @@ export EXPDIR="${EXPDIR:-${HOMEgfs}/parm/config}"
 for config in "${configs[@]:-''}"; do
     source "${EXPDIR}/config.${config}" && true
     export err=$?
+    set +x
     err_chk "FATAL ERROR [${BASH_SOURCE[0]}]: Unable to load config config.${config}"
+    set_trace
 done
 
 
@@ -114,4 +116,6 @@ done
 ##########################################
 source "${HOMEgfs}/env/${machine}.env" "${env_job}" && true
 export err=$?
+set +x
 err_chk "FATAL ERROR: [${BASH_SOURCE[0]}]: Error while sourcing machine environment ${machine}.env for job ${env_job}"
+set_trace