diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6478e3f..be4042d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,7 @@
 - Singularity bind paths were not being set properly. (#119, @kelly-sovacool)
 - Update docker containers to set `$PYTHONPATH`. (#119, #125, @kelly-sovacool)
   - Otherwise, this environment variable can be carried over and cause package conflicts when singularity is not run with `-C`.
+  - Also use `python -E` to ensure the `$PYTHONPATH` is not carried over. (#129, @kelly-sovacool)
 - Fix `reconfig` to correctly replace variables in the config file. (#121, @kelly-sovacool)
 - Prevent using excessive memory when copying reference files. (#126, @kelly-sovacool)
 
diff --git a/workflow/rules/findcircrna.smk b/workflow/rules/findcircrna.smk
index 84712fe..e72dfb4 100644
--- a/workflow/rules/findcircrna.smk
+++ b/workflow/rules/findcircrna.smk
@@ -141,7 +141,7 @@ def get_per_sample_files_to_merge(wildcards):
 # 2. parse the back_spliced_junction BED from above along with known splicing annotations to CircExplorer2 'parse' to create
 #       a. circularRNA_known.txt ... circRNAs around known gene exons
 #       b. low_conf_circularRNA_known.txt .... circRNAs with low confidence
-# 3. parse back_spliced_junction BED along with circularRNA_known.txt and low_conf_circularRNA_known.txt to custom python -E script
+# 3. parse back_spliced_junction BED along with circularRNA_known.txt and low_conf_circularRNA_known.txt to custom python script
 # to create an aggregated list of BSJs with following columns:
 # | # | ColName     |
 # |---|-------------|
@@ -1283,7 +1283,7 @@ rule merge_per_sample:
     container: config['containers']['star_ucsc_cufflinks']
     shell:
         """
-python3 {params.script} \\
+python3 -E {params.script} \\
         --pyscript {params.pyscript} \\
         --dcc {params.ndcc} \\
         --mapsplice {params.nmapsplice} \\
diff --git a/workflow/rules/post_findcircrna_processing.smk b/workflow/rules/post_findcircrna_processing.smk
index f44f6b6..18ef2b7 100644
--- a/workflow/rules/post_findcircrna_processing.smk
+++ b/workflow/rules/post_findcircrna_processing.smk
@@ -74,7 +74,7 @@ BSJbedbn=$(basename {output.BSJbed})
 
 if [ "{params.peorse}" == "PE" ];then
 
-python3 {params.scriptpe} \\
+python3 -E {params.scriptpe} \\
     --inbam {input.chimericbam} \\
     --sample_counts_table {input.countstable} \\
     --plusbam {params.tmpdir}/{params.sample}.BSJ.plus.bam \\
@@ -91,7 +91,7 @@ python3 {params.scriptpe} \\
 
 else
 
-python3 {params.scriptse} \\
+python3 -E {params.scriptse} \\
     --inbam {input.chimericbam} \\
     --sample_counts_table {input.countstable} \\
     --plusbam {params.tmpdir}/{params.sample}.BSJ.plus.bam \\
@@ -127,7 +127,7 @@ for i in $(echo {params.viruses}|tr ',' ' ');do
     bash {params.bam2bwscript} ${{outdir}}/{params.sample}.${{i}}.BSJ.bam {params.tmpdir}
 done
 
-python3 {params.flankscript} --reffa {params.reffa} --inbsjbedgz {params.tmpdir}/${{BSJbedbn}} --outbsjbedgz {output.BSJbed}
+python3 -E {params.flankscript} --reffa {params.reffa} --inbsjbedgz {params.tmpdir}/${{BSJbedbn}} --outbsjbedgz {output.BSJbed}
 
 rm -rf {params.tmpdir}
 """
@@ -283,12 +283,12 @@ rule create_circExplorer_merged_found_counts_table:
         """
         set -exo pipefail
         mkdir -p {params.tmpdir}
-        python3 {params.pythonscript} \\
+        python3 -E {params.pythonscript} \\
             -b {input.bsj_found_counts} \\
             -l {input.linear_spliced_counts} \\
             -o {output.found_counts_table}
 
-        python3 {params.pythonscript2} \\
+        python3 -E {params.pythonscript2} \\
             --annotationcounts {input.annotation_counts} \\
             --allfoundcounts {output.found_counts_table} \\
             --countstable {output.count_counts_table}
@@ -324,9 +324,9 @@ if RUN_MAPSPLICE:
     for bamfile in {input};do
         bamfile_bn=$(basename $bamfile)
         if [ "{params.peorse}" == "PE" ];then
-        echo "python3 {params.bash2nreads_pyscript} --inbam $bamfile --regions {params.regions} --pe > {params.tmpdir}/${{bamfile_bn}}.counts"
+        echo "python3 -E {params.bash2nreads_pyscript} --inbam $bamfile --regions {params.regions} --pe > {params.tmpdir}/${{bamfile_bn}}.counts"
         else
-        echo "python3 {params.bash2nreads_pyscript} --inbam $bamfile --regions {params.regions} > {params.tmpdir}/${{bamfile_bn}}.counts"
+        echo "python3 -E {params.bash2nreads_pyscript} --inbam $bamfile --regions {params.regions} > {params.tmpdir}/${{bamfile_bn}}.counts"
         fi
     done > {params.tmpdir}/do_bamstats
     parallel -j 2 < {params.tmpdir}/do_bamstats
@@ -374,9 +374,9 @@ else:
     for bamfile in {input};do
         bamfile_bn=$(basename $bamfile)
         if [ "{params.peorse}" == "PE" ];then
-        echo "python3 {params.bash2nreads_pyscript} --inbam $bamfile --regions {params.regions} --pe > {params.tmpdir}/${{bamfile_bn}}.counts"
+        echo "python3 -E {params.bash2nreads_pyscript} --inbam $bamfile --regions {params.regions} --pe > {params.tmpdir}/${{bamfile_bn}}.counts"
         else
-        echo "python3 {params.bash2nreads_pyscript} --inbam $bamfile --regions {params.regions} > {params.tmpdir}/${{bamfile_bn}}.counts"
+        echo "python3 -E {params.bash2nreads_pyscript} --inbam $bamfile --regions {params.regions} > {params.tmpdir}/${{bamfile_bn}}.counts"
         fi
     done > {params.tmpdir}/do_bamstats
     parallel -j 2 < {params.tmpdir}/do_bamstats
@@ -450,7 +450,7 @@ rule create_hq_bams:
         outdir=$(dirname {output.outbam})
         if [ ! -d $outdir ];then mkdir -p $outdir;fi
         cd $outdir
-        python3 {params.script} \\
+        python3 -E {params.script} \\
             -i {input.inbam} \\
             -t {input.countstable} \\
             -o {output.outbam} \\
diff --git a/workflow/scripts/_create_circExplorer_linear_bam.v2.sh b/workflow/scripts/_create_circExplorer_linear_bam.v2.sh
index cf44b03..f5f5dc4 100755
--- a/workflow/scripts/_create_circExplorer_linear_bam.v2.sh
+++ b/workflow/scripts/_create_circExplorer_linear_bam.v2.sh
@@ -42,7 +42,7 @@ start0=$(date +%s.%N)
     # _bedintersect_to_rid2jid.py
 # also requires these tools
     # bedtools
-    # python3 with pysam library
+    # python3 -E with pysam library
     # samtools
     # bedSort from ucsc tools
     # ucsc
@@ -126,14 +126,14 @@ start=$(date +%s.%N)
 
 if [ "$peorse" == "PE" ];then
 
-python3 ${SCRIPT_DIR}/filter_bam.py \
+python3 -E ${SCRIPT_DIR}/filter_bam.py \
     --inbam $non_chimeric_star2p_bam \
     --outbam $filtered_bam \
     --pe
 
 else
 
-python3 ${SCRIPT_DIR}/filter_bam.py \
+python3 -E ${SCRIPT_DIR}/filter_bam.py \
     --inbam $non_chimeric_star2p_bam \
     --outbam $filtered_bam \
 
@@ -183,7 +183,7 @@ bedSort ${tmpdir}/BSJ.ends.bed ${tmpdir}/BSJ.ends.bed
 printtime $SCRIPT_NAME $start0 $start "finding max readlength"
 start=$(date +%s.%N)
 
-python3 ${SCRIPT_DIR}/bam_get_max_readlen.py -i $filtered_bam > ${tmpdir}/${sample_name}.maxrl
+python3 -E ${SCRIPT_DIR}/bam_get_max_readlen.py -i $filtered_bam > ${tmpdir}/${sample_name}.maxrl
 maxrl=$(cat ${tmpdir}/${sample_name}.maxrl)
 two_maxrl=$((maxrl*2))
 
@@ -226,7 +226,7 @@ pigz -p4 -f ${rid2jidgzip%.*} && rm -f ${rid2jidgzip%.*}.tmp
 printtime $SCRIPT_NAME $start0 $start "filter linear and spliced readids to those near BSJs only; creating counts table"
 start=$(date +%s.%N)
 
-python3 ${SCRIPT_DIR}/_filter_linear_spliced_readids_w_rid2jid.py \
+python3 -E ${SCRIPT_DIR}/_filter_linear_spliced_readids_w_rid2jid.py \
     --linearin ${tmpdir}/${sample_name}.linear.readids.gz \
     --splicedin ${tmpdir}/${sample_name}.spliced.readids.gz \
     --rid2jid ${rid2jidgzip} \
@@ -254,10 +254,10 @@ splicedbam_bn=$(basename $splicedbam)
 linearbam_all_bn=$(basename $linearbam_all)
 splicedbam_all_bn=$(basename $splicedbam_all)
 
-echo "python3 ${SCRIPT_DIR}/filter_bam_by_readids.py --inputBAM $filtered_bam --outputBAM ${tmpdir}/${linearbam_bn} --readids $linearrids" >> ${tmpdir}/para2
-echo "python3 ${SCRIPT_DIR}/filter_bam_by_readids.py --inputBAM $filtered_bam --outputBAM ${tmpdir}/${splicedbam_bn} --readids $splicedrids" >> ${tmpdir}/para2
-echo "python3 ${SCRIPT_DIR}/filter_bam_by_readids.py --inputBAM $filtered_bam --outputBAM ${tmpdir}/${linearbam_all_bn} --readids ${tmpdir}/${sample_name}.linear.readids.gz" >> ${tmpdir}/para2
-echo "python3 ${SCRIPT_DIR}/filter_bam_by_readids.py --inputBAM $filtered_bam --outputBAM ${tmpdir}/${splicedbam_all_bn} --readids ${tmpdir}/${sample_name}.spliced.readids.gz" >> ${tmpdir}/para2
+echo "python3 -E ${SCRIPT_DIR}/filter_bam_by_readids.py --inputBAM $filtered_bam --outputBAM ${tmpdir}/${linearbam_bn} --readids $linearrids" >> ${tmpdir}/para2
+echo "python3 -E ${SCRIPT_DIR}/filter_bam_by_readids.py --inputBAM $filtered_bam --outputBAM ${tmpdir}/${splicedbam_bn} --readids $splicedrids" >> ${tmpdir}/para2
+echo "python3 -E ${SCRIPT_DIR}/filter_bam_by_readids.py --inputBAM $filtered_bam --outputBAM ${tmpdir}/${linearbam_all_bn} --readids ${tmpdir}/${sample_name}.linear.readids.gz" >> ${tmpdir}/para2
+echo "python3 -E ${SCRIPT_DIR}/filter_bam_by_readids.py --inputBAM $filtered_bam --outputBAM ${tmpdir}/${splicedbam_all_bn} --readids ${tmpdir}/${sample_name}.spliced.readids.gz" >> ${tmpdir}/para2
 
 parallel -j 4 < ${tmpdir}/para2
 
@@ -283,10 +283,10 @@ samtools sort -l 9 -T ${tmpdir}/sorttmp --write-index -@${threads} -O BAM -o ${s
 
 if [ -f ${tmpdir}/para3 ];then rm -f ${tmpdir}/para3;fi
 
-echo "python3 ${SCRIPT_DIR}/bam_split_by_regions.py --inbam $linearbam --sample_name $sample_name --regions $regions --prefix linear_BSJ --outdir $outdir --host $host --additives $additives --viruses $viruses" >> ${tmpdir}/para3
-echo "python3 ${SCRIPT_DIR}/bam_split_by_regions.py --inbam $splicedbam --sample_name $sample_name --regions $regions --prefix spliced_BSJ --outdir $outdir --host $host --additives $additives --viruses $viruses" >> ${tmpdir}/para3
-echo "python3 ${SCRIPT_DIR}/bam_split_by_regions.py --inbam $linearbam_all --sample_name $sample_name --regions $regions --prefix linear --outdir $outdir --host $host --additives $additives --viruses $viruses" >> ${tmpdir}/para3
-echo "python3 ${SCRIPT_DIR}/bam_split_by_regions.py --inbam $splicedbam_all --sample_name $sample_name --regions $regions --prefix spliced --outdir $outdir --host $host --additives $additives --viruses $viruses" >> ${tmpdir}/para3
+echo "python3 -E ${SCRIPT_DIR}/bam_split_by_regions.py --inbam $linearbam --sample_name $sample_name --regions $regions --prefix linear_BSJ --outdir $outdir --host $host --additives $additives --viruses $viruses" >> ${tmpdir}/para3
+echo "python3 -E ${SCRIPT_DIR}/bam_split_by_regions.py --inbam $splicedbam --sample_name $sample_name --regions $regions --prefix spliced_BSJ --outdir $outdir --host $host --additives $additives --viruses $viruses" >> ${tmpdir}/para3
+echo "python3 -E ${SCRIPT_DIR}/bam_split_by_regions.py --inbam $linearbam_all --sample_name $sample_name --regions $regions --prefix linear --outdir $outdir --host $host --additives $additives --viruses $viruses" >> ${tmpdir}/para3
+echo "python3 -E ${SCRIPT_DIR}/bam_split_by_regions.py --inbam $splicedbam_all --sample_name $sample_name --regions $regions --prefix spliced --outdir $outdir --host $host --additives $additives --viruses $viruses" >> ${tmpdir}/para3
 
 parallel -j 4 < ${tmpdir}/para3
 
diff --git a/workflow/scripts/_make_merge_per_sample_sh.py b/workflow/scripts/_make_merge_per_sample_sh.py
index 1b1365f..5c248f5 100755
--- a/workflow/scripts/_make_merge_per_sample_sh.py
+++ b/workflow/scripts/_make_merge_per_sample_sh.py
@@ -1,78 +1,154 @@
 import argparse
 from os.path import join
 
-def _get_counts_file_path(sampledir,s,prog):
-    if prog=="circExplorer":
-        return join(sampledir,"circExplorer",s+".circExplorer.counts_table.tsv")
-    if prog=="circExplorerbwa":
-        return join(sampledir,"circExplorer_BWA",s+".circExplorer_bwa.annotation_counts.tsv")
-    elif prog=="ciri":
-        return join(sampledir,"ciri",s+".ciri.out.filtered")
-    elif prog=="dcc":
-        return join(sampledir,"DCC",s+".dcc.counts_table.tsv.filtered")
-    elif prog=="mapsplice":
-        return join(sampledir,"MapSplice",s+".mapsplice.counts_table.tsv.filtered")
-    elif prog=="nclscan":
-        return join(sampledir,"NCLscan",s+".nclscan.counts_table.tsv.filtered")
-    elif prog=="circrnafinder":
-        return join(sampledir,"circRNA_finder",s+".circRNA_finder.counts_table.tsv.filtered")
-    elif prog=="findcirc":
-        return join(sampledir,"find_circ",s+".find_circ.bed.filtered")
 
+def _get_counts_file_path(sampledir, s, prog):
+    if prog == "circExplorer":
+        return join(sampledir, "circExplorer", s + ".circExplorer.counts_table.tsv")
+    if prog == "circExplorerbwa":
+        return join(
+            sampledir, "circExplorer_BWA", s + ".circExplorer_bwa.annotation_counts.tsv"
+        )
+    elif prog == "ciri":
+        return join(sampledir, "ciri", s + ".ciri.out.filtered")
+    elif prog == "dcc":
+        return join(sampledir, "DCC", s + ".dcc.counts_table.tsv.filtered")
+    elif prog == "mapsplice":
+        return join(sampledir, "MapSplice", s + ".mapsplice.counts_table.tsv.filtered")
+    elif prog == "nclscan":
+        return join(sampledir, "NCLscan", s + ".nclscan.counts_table.tsv.filtered")
+    elif prog == "circrnafinder":
+        return join(
+            sampledir, "circRNA_finder", s + ".circRNA_finder.counts_table.tsv.filtered"
+        )
+    elif prog == "findcirc":
+        return join(sampledir, "find_circ", s + ".find_circ.bed.filtered")
 
-def main() :
-    parser = argparse.ArgumentParser(description='Merge per sample Counts from different circRNA detection tools')
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Merge per sample Counts from different circRNA detection tools"
+    )
     # INPUTS
-    parser.add_argument('--pyscript', dest='pyscript', type=str, required=True,
-        help='python script to be run')
-    parser.add_argument('--sampledir', dest='sampledir', type=str, required=True,
-        help='generally <workdir>/<results>/<sampleName>')
-    parser.add_argument('--dcc', dest='dcc', type=int, required=False, default=0,
-        help='n_run_dcc')
-    parser.add_argument('--mapsplice', dest='mapsplice', type=int, required=False,default=0,
-        help='n_run_mapslice')
-    parser.add_argument('--findcirc', dest='findcirc', type=int, required=False,default=0,
-        help='n_run_findcirc')
-    parser.add_argument('--nclscan', dest='nclscan', type=int, required=False,default=0,
-        help='n_run_nclscan')
-    parser.add_argument('--circrnafinder', dest='circrnafinder', type=int, required=False, default=0,
-        help='n_run_circrnafinder')
-    parser.add_argument('--samplename', dest='samplename', type=str, required=True,
-        help='Sample Name')
-    parser.add_argument('--min_read_count_reqd', dest='minreads', type=int, required=False, default=2,
-        help='Read count threshold..circRNA with lower than this number of read support are excluded! (default=2)')
-    parser.add_argument('--hqcc', dest='hqcc', type=str, required=False, default="circExplorer,circExplorer_bwa",
-        help='Comma separated list of high confidence core callers (default="circExplorer,circExplorer_bwa")')
-    parser.add_argument('--hqccpn', dest='hqccpn', type=int, required=False, default=1,
-        help='Define n:high confidence core callers plus n callers are required to call this circRNA HQ (default 1)')
-    parser.add_argument("--reffa",dest="reffa",required=True,type=str,
-        help="reference fasta file path")
-    parser.add_argument('--pyscriptoutfile',required=True,help='merged table')
+    parser.add_argument(
+        "--pyscript",
+        dest="pyscript",
+        type=str,
+        required=True,
+        help="python script to be run",
+    )
+    parser.add_argument(
+        "--sampledir",
+        dest="sampledir",
+        type=str,
+        required=True,
+        help="generally <workdir>/<results>/<sampleName>",
+    )
+    parser.add_argument(
+        "--dcc", dest="dcc", type=int, required=False, default=0, help="n_run_dcc"
+    )
+    parser.add_argument(
+        "--mapsplice",
+        dest="mapsplice",
+        type=int,
+        required=False,
+        default=0,
+        help="n_run_mapslice",
+    )
+    parser.add_argument(
+        "--findcirc",
+        dest="findcirc",
+        type=int,
+        required=False,
+        default=0,
+        help="n_run_findcirc",
+    )
+    parser.add_argument(
+        "--nclscan",
+        dest="nclscan",
+        type=int,
+        required=False,
+        default=0,
+        help="n_run_nclscan",
+    )
+    parser.add_argument(
+        "--circrnafinder",
+        dest="circrnafinder",
+        type=int,
+        required=False,
+        default=0,
+        help="n_run_circrnafinder",
+    )
+    parser.add_argument(
+        "--samplename", dest="samplename", type=str, required=True, help="Sample Name"
+    )
+    parser.add_argument(
+        "--min_read_count_reqd",
+        dest="minreads",
+        type=int,
+        required=False,
+        default=2,
+        help="Read count threshold..circRNA with lower than this number of read support are excluded! (default=2)",
+    )
+    parser.add_argument(
+        "--hqcc",
+        dest="hqcc",
+        type=str,
+        required=False,
+        default="circExplorer,circExplorer_bwa",
+        help='Comma separated list of high confidence core callers (default="circExplorer,circExplorer_bwa")',
+    )
+    parser.add_argument(
+        "--hqccpn",
+        dest="hqccpn",
+        type=int,
+        required=False,
+        default=1,
+        help="Define n:high confidence core callers plus n callers are required to call this circRNA HQ (default 1)",
+    )
+    parser.add_argument(
+        "--reffa",
+        dest="reffa",
+        required=True,
+        type=str,
+        help="reference fasta file path",
+    )
+    parser.add_argument("--pyscriptoutfile", required=True, help="merged table")
     # OUTPUTS
-    parser.add_argument('--outscript',required=True,help='output bash script')
+    parser.add_argument("--outscript", required=True, help="output bash script")
     args = parser.parse_args()
-    
-    sd=args.sampledir
-    sn=args.samplename
-    parameters=""
-    parameters+=" --circExplorer "+_get_counts_file_path(sd,sn,'circExplorer')
-    parameters+=" --ciri "+_get_counts_file_path(sd,sn,'ciri')
-    parameters+=" --circExplorerbwa "+_get_counts_file_path(sd,sn,'circExplorerbwa')
-    if args.dcc==1: parameters+=" --dcc "+_get_counts_file_path(sd,sn,'dcc')
-    if args.mapsplice==1: parameters+=" --mapsplice "+_get_counts_file_path(sd,sn,'mapsplice')
-    if args.nclscan==1: parameters+=" --nclscan "+_get_counts_file_path(sd,sn,'nclscan')
-    if args.circrnafinder==1: parameters+=" --circrnafinder "+_get_counts_file_path(sd,sn,'circrnafinder')
-    if args.findcirc==1: parameters+=" --findcirc "+_get_counts_file_path(sd,sn,'findcirc')
-    parameters+=" --reffa "+args.reffa
-    parameters+=" --min_read_count_reqd "+str(args.minreads)
-    parameters+=" --samplename "+sn
-    parameters+=" --hqcc "+args.hqcc
-    parameters+=" --hqccpn "+str(args.hqccpn)
-    parameters+=" -o "+args.pyscriptoutfile
-    
-    with open(args.outscript,'w') as outscript:
-        outscript.write("python3 "+args.pyscript+parameters)
+
+    sd = args.sampledir
+    sn = args.samplename
+    parameters = ""
+    parameters += " --circExplorer " + _get_counts_file_path(sd, sn, "circExplorer")
+    parameters += " --ciri " + _get_counts_file_path(sd, sn, "ciri")
+    parameters += " --circExplorerbwa " + _get_counts_file_path(
+        sd, sn, "circExplorerbwa"
+    )
+    if args.dcc == 1:
+        parameters += " --dcc " + _get_counts_file_path(sd, sn, "dcc")
+    if args.mapsplice == 1:
+        parameters += " --mapsplice " + _get_counts_file_path(sd, sn, "mapsplice")
+    if args.nclscan == 1:
+        parameters += " --nclscan " + _get_counts_file_path(sd, sn, "nclscan")
+    if args.circrnafinder == 1:
+        parameters += " --circrnafinder " + _get_counts_file_path(
+            sd, sn, "circrnafinder"
+        )
+    if args.findcirc == 1:
+        parameters += " --findcirc " + _get_counts_file_path(sd, sn, "findcirc")
+    parameters += " --reffa " + args.reffa
+    parameters += " --min_read_count_reqd " + str(args.minreads)
+    parameters += " --samplename " + sn
+    parameters += " --hqcc " + args.hqcc
+    parameters += " --hqccpn " + str(args.hqccpn)
+    parameters += " -o " + args.pyscriptoutfile
+
+    with open(args.outscript, "w") as outscript:
+        outscript.write("python3 -E " + args.pyscript + parameters)
     outscript.close()
 
+
 if __name__ == "__main__":
-    main()
\ No newline at end of file
+    main()