diff --git a/Snakefile b/Snakefile
index 953a9f0..d7962ed 100644
--- a/Snakefile
+++ b/Snakefile
@@ -16,10 +16,6 @@ def _get_seqdir(wildcards):
     return os.path.dirname(samples.loc[(wildcards.sample), ["assembly"]].dropna()[0])
 
 rule all:
-    input:
-        "pipeline_finished.txt"
-
-rule cleanup:
     input:
         expand("results/{sample}/amrplusplus/{amrplusplus_outputs}", sample=samples.index, amrplusplus_outputs=amrplusplus_exts),
         expand("results/{sample}/rgi/rgi.json", sample=samples.index),
@@ -32,18 +28,11 @@ rule cleanup:
         expand("results/{sample}/resfams/resfams.tblout", sample=samples.index),
         expand("results/{sample}/mykrobe/report.json", sample=samples.index),
         expand("results/{sample}/resfinder/data_resfinder.json", sample=samples.index),
-        expand("results/{sample}/srax/Results/sraX_analysis.html", sample=samples.index),
+        expand("results/{sample}/srax/sraX_analysis.html", sample=samples.index),
         expand("results/{sample}/sstar/report.tsv", sample=samples.index),
         expand("results/{sample}/kmerresistance/results.KmerRes", sample=samples.index),
         expand("results/{sample}/deeparg/output.mapping.ARG", sample=samples.index),
         #expand("results/{sample}/srst2/srst2__fullgenes__ResFinder__results.txt", sample=samples.index)
-    output:
-        "pipeline_finished.txt"
-    shell:
-        """
-        rm -r results/*/groot/graphs results/*/deeparg/*.fasta results/*/amrplusplus/tmp results/*/staramr/hits/ results/*/ariba/*.gz results/*/srax/tmp results/*/mykrobe/skels || echo "tempfiles already absent"
-        touch pipeline_finished.txt
-        """
 
 #include: "rules/srst2.smk" 
 include: "rules/deeparg.smk"
diff --git a/rules/abricate.smk b/rules/abricate.smk
index e323717..1316d4a 100644
--- a/rules/abricate.smk
+++ b/rules/abricate.smk
@@ -17,5 +17,5 @@ rule run_abricate:
     shell:
         """
         abricate --list > {log}
-        abricate --threads {threads} --nopath --db {params.dbname} --minid {params.minid} --mincov {params.mincov} {input.contigs} > {output.report} 2> >(tee -a {log} >&2)
+        abricate --threads {threads} --nopath --db {params.dbname} --minid {params.minid} --mincov {params.mincov} {input.contigs} > {output.report} > {log} 2>&1
         """
diff --git a/rules/amrfinder.smk b/rules/amrfinder.smk
index 8c7e4e4..7f6fbfb 100644
--- a/rules/amrfinder.smk
+++ b/rules/amrfinder.smk
@@ -20,8 +20,12 @@ rule run_amrfinder:
     conda:
       "../envs/amrfinder.yaml"
     params:
-        organism = config["params"]["amrfinder"]["organism"]
+        organism = config["params"]["amrfinder"]["organism"],
+        output_tmp_dir = "results/{sample}/amrfinder/tmp"
     threads:
        config["params"]["threads"]
     shell:
-       "amrfinder -n {input.contigs} -o {output.report} -O {params.organism} -d {input.db}/latest 2> >(tee {log} >&2) "
+        """
+        amrfinder -n {input.contigs} -o {output.report} -O {params.organism} -d {input.db}/latest >{log} 2>&1
+        rm -rf {params.output_tmp_dir}
+        """
diff --git a/rules/amrplusplus.smk b/rules/amrplusplus.smk
index e3e1822..14bd2ba 100644
--- a/rules/amrplusplus.smk
+++ b/rules/amrplusplus.smk
@@ -66,9 +66,10 @@ rule run_amrplusplus:
     shell:
        """
        mkdir -p {params.output_prefix_tmp}
-       trimmomatic PE  {input.read1} {input.read2} {params.output_prefix_tmp}/{wildcards.sample}_r1_pe_trimmed.fq {params.output_prefix_tmp}/{wildcards.sample}_r1_se_trimmed.fq {params.output_prefix_tmp}/{wildcards.sample}_r2_pe_trimmed.fq {params.output_prefix_tmp}/{wildcards.sample}_r2_se_trimmed.fq SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:36 2> >(tee {log} >&2)
-       bwa mem {input.megares_db} {params.output_prefix_tmp}/{wildcards.sample}_r1_pe_trimmed.fq {params.output_prefix_tmp}/{wildcards.sample}_r2_pe_trimmed.fq | samtools sort -n -O sam > {params.output_prefix_tmp}/{wildcards.sample}.sam 2> >(tee -a {log} >&2)
-       {input.resistome_tool} -ref_fp {input.megares_db} -annot_fp {input.megares_annot} -sam_fp {params.output_prefix_tmp}/{wildcards.sample}.sam -gene_fp {output.amr_gene} -group_fp {output.amr_group} -class_fp {output.amr_class} -mech_fp {output.amr_mech} -t 80 2> >(tee -a {log} >&2)
-       {input.rarefaction_tool} -ref_fp {input.megares_db} -annot_fp {input.megares_annot} -sam_fp {params.output_prefix_tmp}/{wildcards.sample}.sam -gene_fp {output.amr_gene}_rare -group_fp {output.amr_group}_rare -class_fp {output.amr_class}_rare -mech_fp {output.amr_mech}_rare -min 5 -max 100 -skip 5 -samples 1 -t 80 2> >(tee -a {log} >&2)
-       {input.snp_tool} -amr_fp {input.megares_db} -sampe {params.output_prefix_tmp}/{wildcards.sample}.sam -out_fp {output.amr_snps} 2> >(tee -a {log} >&2)
+       trimmomatic PE  {input.read1} {input.read2} {params.output_prefix_tmp}/{wildcards.sample}_r1_pe_trimmed.fq {params.output_prefix_tmp}/{wildcards.sample}_r1_se_trimmed.fq {params.output_prefix_tmp}/{wildcards.sample}_r2_pe_trimmed.fq {params.output_prefix_tmp}/{wildcards.sample}_r2_se_trimmed.fq SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:36 >{log} 2>&1 
+       bwa mem {input.megares_db} {params.output_prefix_tmp}/{wildcards.sample}_r1_pe_trimmed.fq {params.output_prefix_tmp}/{wildcards.sample}_r2_pe_trimmed.fq 2>> {log} | samtools sort -n -O sam > {params.output_prefix_tmp}/{wildcards.sample}.sam 2>>{log}
+       {input.resistome_tool} -ref_fp {input.megares_db} -annot_fp {input.megares_annot} -sam_fp {params.output_prefix_tmp}/{wildcards.sample}.sam -gene_fp {output.amr_gene} -group_fp {output.amr_group} -class_fp {output.amr_class} -mech_fp {output.amr_mech} -t 80  >>{log} 2>&1
+       {input.rarefaction_tool} -ref_fp {input.megares_db} -annot_fp {input.megares_annot} -sam_fp {params.output_prefix_tmp}/{wildcards.sample}.sam -gene_fp {output.amr_gene}_rare -group_fp {output.amr_group}_rare -class_fp {output.amr_class}_rare -mech_fp {output.amr_mech}_rare -min 5 -max 100 -skip 5 -samples 1 -t 80 >>{log} 2>&1
+       {input.snp_tool} -amr_fp {input.megares_db} -sampe {params.output_prefix_tmp}/{wildcards.sample}.sam -out_fp {output.amr_snps} >>{log} 2>&1
+       rm -rf {params.output_prefix_tmp}
        """
diff --git a/rules/ariba.smk b/rules/ariba.smk
index e29cbed..daac8af 100644
--- a/rules/ariba.smk
+++ b/rules/ariba.smk
@@ -25,12 +25,11 @@ rule run_ariba:
        "logs/ariba_{sample}.log"
     conda:
       "../envs/ariba.yaml"
-    threads:
-       config["params"]["threads"]
+    threads: 1
     params:
         output_folder = "results/{sample}/ariba/"
     shell:
        """
-       rm -r {params.output_folder};
-       ariba run --threads 1 {input.ref_db} {input.read1} {input.read2} {params.output_folder} 2> >(tee {log} >&2)
+       rm -r {params.output_folder}
+       ariba run --threads {threads} {input.ref_db} {input.read1} {input.read2} {params.output_folder} > {log} 2>&1
        """
diff --git a/rules/deeparg.smk b/rules/deeparg.smk
index 1243e18..14811f2 100644
--- a/rules/deeparg.smk
+++ b/rules/deeparg.smk
@@ -4,11 +4,14 @@ rule run_deeparg:
     output:
         report = "results/{sample}/deeparg/output.mapping.ARG",
         report_potential = "results/{sample}/deeparg/output.mapping.potential.ARG"
+    log:
+       "logs/amrfinder_{sample}.log"
     singularity:
         "docker://gaarangoa/deeparg:v1.0.1"
     shell:
         """
-        python /deeparg/deepARG.py --align --type nucl --reads --input /data/results/{wildcards.sample}/deeparg/reads.fasta --output /data/results/{wildcards.sample}/deeparg/output
+        python /deeparg/deepARG.py --align --type nucl --reads --input /data/results/{wildcards.sample}/deeparg/reads.fasta --output /data/results/{wildcards.sample}/deeparg/output > {log} 2>&1
+        rm /data/results/{wildcards.sample}/deeparg/reads.fasta
         """
 
 rule prepare_deeparg_reads:
diff --git a/rules/groot.smk b/rules/groot.smk
index 809d1f6..179d55a 100644
--- a/rules/groot.smk
+++ b/rules/groot.smk
@@ -36,4 +36,7 @@ rule run_groot:
         max_read_length = config['params']['groot']['read_length'] + 5,
         graph_dir = "results/{sample}/groot/graphs"
     shell:
-       "zcat {input.read1} {input.read2} | seqkit seq --min-len {params.min_read_length} --max-len {params.max_read_length} | groot align -g {params.graph_dir} -p {threads} -i {input.db_index} --log {log} | groot report --log {log} > {output.report}"
+       """
+       zcat {input.read1} {input.read2} | seqkit seq --min-len {params.min_read_length} --max-len {params.max_read_length} | groot align -g {params.graph_dir} -p {threads} -i {input.db_index} --log {log} | groot report --log {log} > {output.report}
+       rm -rf {params.graph_dir}
+       """
diff --git a/rules/kmerresistance.smk b/rules/kmerresistance.smk
index f40a9c2..4338829 100644
--- a/rules/kmerresistance.smk
+++ b/rules/kmerresistance.smk
@@ -51,6 +51,6 @@ rule run_kmerresistance:
     shell:
        """
        zcat {input.read1} {input.read2} > {params.output_folder}/temp_all_reads.fq
-       kmerresistance -i {params.output_folder}/temp_all_reads.fq -t_db {params.kma_resfinder_db} -s_db {params.species_db} -o {params.output_folder}/results 2> >(tee {log} >&2)
+       kmerresistance -i {params.output_folder}/temp_all_reads.fq -t_db {params.kma_resfinder_db} -s_db {params.species_db} -o {params.output_folder}/results > {log} 2>&1
        rm {params.output_folder}/temp_all_reads.fq
        """
diff --git a/rules/mykrobe.smk b/rules/mykrobe.smk
index 10810b9..5a2989f 100644
--- a/rules/mykrobe.smk
+++ b/rules/mykrobe.smk
@@ -13,6 +13,10 @@ rule run_mykrobe:
        config["params"]["threads"]
     params:
         tmp = "results/{sample}/mykrobe/tmp/",
-        skel_dir = "results/{sample}/mykrobe/skels"
+        skel_dir = "results/{sample}/mykrobe/skels",
+        tmp_dir = "results/{sample}/mykrobe/tmp"
     shell:
-       "mykrobe predict {wildcards.sample} tb -1 {input.read1} {input.read2} --skeleton_dir {params.skel_dir} --threads {threads} --format json --output {output.report} --tmp {params.tmp} 2> >(tee {log} >&2) "
+       """
+       mykrobe predict {wildcards.sample} tb -1 {input.read1} {input.read2} --skeleton_dir {params.skel_dir} --threads {threads} --format json --output {output.report} --tmp {params.tmp} > {log} 2>&1
+       rm -rf {params.skel_dir} {params.tmp_dir}
+       """
diff --git a/rules/pointfinder.smk b/rules/pointfinder.smk
index 28629db..97d3123 100644
--- a/rules/pointfinder.smk
+++ b/rules/pointfinder.smk
@@ -38,9 +38,10 @@ rule run_pointfinder:
         config["params"]["threads"]
     params:
         species = config["params"]["pointfinder"]["species"],
-        
+        output_tmp_dir = "results/{sample}/pointfinder/tmp"
     shell:
         """
-        python {input.pointfinder_script} -i {input.contigs} -p {input.pointfinder_db} -s {params.species} -m blastn -m_p $(which blastn) -o results/{wildcards.sample}/pointfinder 2> >(tee {log} >&2)
+        python {input.pointfinder_script} -i {input.contigs} -p {input.pointfinder_db} -s {params.species} -m blastn -m_p $(which blastn) -o results/{wildcards.sample}/pointfinder > {log} 2>&1
         cp {output.raw_report} {output.report}
+        rm -rf {params.output_tmp_dir}
         """
diff --git a/rules/resfams.smk b/rules/resfams.smk
index 3660d71..8dafc11 100644
--- a/rules/resfams.smk
+++ b/rules/resfams.smk
@@ -21,6 +21,6 @@ rule run_resfams:
         output_prefix = "results/{sample}/resfams"
     shell:
        """
-       prodigal -i {input.contigs} -a {params.output_prefix}/protein_seqs.faa 2> >(tee {log} >&2);
-       hmmsearch --cpu {threads} --tblout {output.report} {input.resfams_hmms} {params.output_prefix}/protein_seqs.faa  > {log} 2>&1
+       prodigal -i {input.contigs} -a {params.output_prefix}/protein_seqs.faa > {log} 2>&1
+       hmmsearch --cpu {threads} --tblout {output.report} {input.resfams_hmms} {params.output_prefix}/protein_seqs.faa  >>{log} 2>&1
        """
diff --git a/rules/resfinder.smk b/rules/resfinder.smk
index 19cb7aa..9786a7b 100644
--- a/rules/resfinder.smk
+++ b/rules/resfinder.smk
@@ -25,9 +25,11 @@ rule run_resfinder:
     threads:
        config["params"]["threads"]
     params:
-        outdir = "results/{sample}/resfinder"
+        outdir = "results/{sample}/resfinder",
+        output_tmp_dir = "results/{sample}/resfinder/tmp"
     shell:
        """
-       mkdir -p {params.outdir};
-       resfinder.py -p {input.resfinder_db} -i {input.contigs} -o {params.outdir} 2> >(tee {log} >&2)
+       mkdir -p {params.outdir}
+       resfinder.py -p {input.resfinder_db} -i {input.contigs} -o {params.outdir} > {log} 2>&1
+       rm -rf {params.output_tmp_dir}
        """
diff --git a/rules/rgi.smk b/rules/rgi.smk
index 4e37a1d..d98276b 100644
--- a/rules/rgi.smk
+++ b/rules/rgi.smk
@@ -30,6 +30,6 @@ rule run_rgi:
         output_prefix = "results/{sample}/rgi/rgi"
     shell:
        """
-       rgi load --card_json {input.card_db}
-       rgi main --input_sequence {input.contigs} --output_file {params.output_prefix} --clean --num_threads {threads} 2> >(tee {log} >&2)
+       rgi load --card_json {input.card_db} > {log} 2>&1
+       rgi main --input_sequence {input.contigs} --output_file {params.output_prefix} --clean --num_threads {threads} >>{log} 2>&1
        """
diff --git a/rules/srax.smk b/rules/srax.smk
index ef474ae..886ba7c 100644
--- a/rules/srax.smk
+++ b/rules/srax.smk
@@ -2,7 +2,7 @@ rule run_srax:
     input:
         genome_dir = lambda wildcards: _get_seqdir(wildcards),
     output:
-        report = "results/{sample}/srax/Results/sraX_analysis.html"
+        report = "results/{sample}/srax/sraX_analysis.html"
     message: "Running rule run_srax on {wildcards.sample} with contigs"
     log:
        "logs/srax_{sample}.log"
@@ -12,6 +12,15 @@ rule run_srax:
        config["params"]["threads"]
     params:
        dbtype = config["params"]["srax"]["dbtype"],
-       outdir = "results/{sample}/srax"
+       outdir = "results/{sample}/srax",
+       tmp_output_dir = "results/{sample}/srax/tmp",
+       log_output_dir = "results/{sample}/srax/Log",
+       ARG_DB_output_dir = "results/{sample}/srax/ARG_DB",
+       analysis_output_dir = "results/{sample}/srax/Analysis",
+       result_output_dir = "results/{sample}/srax/Results"
     shell:
-       "sraX -i {input.genome_dir} -t 4 -db {params.dbtype} -o {params.outdir} 2> >(tee {log} >&2)"
+       """
+       sraX -i {input.genome_dir} -t 4 -db {params.dbtype} -o {params.outdir} > {log} 2>&1
+       mv {params.result_output_dir}/* {params.outdir}
+       rm -rf {params.tmp_output_dir} {params.log_output_dir} {params.ARG_DB_output_dir} {params.analysis_output_dir} {params.result_output_dir}
+       """
diff --git a/rules/srst2.smk b/rules/srst2.smk
index 9b3d2f0..4e2a6b5 100644
--- a/rules/srst2.smk
+++ b/rules/srst2.smk
@@ -17,4 +17,4 @@ rule run_srst2:
         max_divergence = config["params"]["srst2"]["max_divergence"],
         output_prefix = "results/{sample}/srst2/srst2"
     shell:
-       "srst2 --threads {threads} --gene_db {params.gene_db} --forward '_R1' --reverse '_R2' --input_pe {input.read1} {input.read2} --min_depth {params.min_depth} --output {params.output_prefix} 2> >(tee {log} >&2)"
+       "srst2 --threads {threads} --gene_db {params.gene_db} --forward '_R1' --reverse '_R2' --input_pe {input.read1} {input.read2} --min_depth {params.min_depth} --output {params.output_prefix} > {log} 2>&1"
diff --git a/rules/sstar.smk b/rules/sstar.smk
index 7ac4689..585a4c6 100644
--- a/rules/sstar.smk
+++ b/rules/sstar.smk
@@ -35,5 +35,5 @@ rule run_sstar:
         outdir = 'results/{sample}/sstar'
     shell:
        """
-       {input.sstar} -g {input.contigs} -d {input.resgannot_db} --outdir {params.outdir} > {output.report} 
+       {input.sstar} -g {input.contigs} -d {input.resgannot_db} --outdir {params.outdir} > {output.report} 2>{log}
        """
diff --git a/rules/staramr.smk b/rules/staramr.smk
index 8139c8a..e95a750 100644
--- a/rules/staramr.smk
+++ b/rules/staramr.smk
@@ -16,6 +16,6 @@ rule run_staramr:
     shell:
        """
        rm -r {params.output_folder};
-       staramr search -o {params.output_folder} --nproc {threads} {input.contigs} 2> >(tee {log} >&2)
+       staramr search -o {params.output_folder} --nproc {threads} {input.contigs} >{log} 2>&1
        """
         # only support salmonella/campylobacter