diff --git a/SUBMIT_CONFIG/slurm/cluster.yaml b/SUBMIT_CONFIG/slurm/cluster.yaml
index fb3e45ed39a1d486b6ac0682de054e5293db3d41..d50e4dfc51ff26a0421d4416492282c494e54aee 100644
--- a/SUBMIT_CONFIG/slurm/cluster.yaml
+++ b/SUBMIT_CONFIG/slurm/cluster.yaml
@@ -1,39 +1,38 @@
 __default__:
     jobname:    'GEP.{rule}'
-    partition:  begendiv
+    partition:  begendiv,main
     nCPUs:      "{threads}"
     qos:        'standard'
-    nodes: 1
 
 
 unzipFasta_PRI:
     jobname:    GEP.{rule}.{wildcards.asmID}
     memory:     500
-    time:       "00:00:05"
+    time:       "00:05:00"
 
 symlinkUnzippedFasta_PRI:
     jobname:    GEP.{rule}.{wildcards.asmID}
     memory:     500
-    time:       "00:00:05"
+    time:       "00:05:00"
 
 
 unzipFasta_ALT:
     jobname:    GEP.{rule}.{wildcards.asmID}
     memory:     500
-    time:       "00:00:05"
+    time:       "00:05:00"
 
 
 
 symlinkUnzippedFasta_ALT:
     jobname:    GEP.{rule}.{wildcards.asmID}
     memory:     500
-    time:       "00:00:05"
+    time:       "00:05:05"
 
 
 
 busco5:
     jobname:    GEP.{rule}.{wildcards.asmID}
-    memory:     100000
+    memory:     150000
     time:       "1-00:00:00"
 
 
@@ -41,14 +40,14 @@ busco5:
 moveBuscoOutputs:
     jobname:    GEP.{rule}.{wildcards.asmID}
     memory:     500
-    time:       "00:00:05"
+    time:       "00:05:05"
 
 
 
 
 merqury:
     jobname:    GEP.{rule}.{wildcards.asmID}
-    memory:     20000
+    memory:     40000
     time:       "08:00:00"
 
 
@@ -56,50 +55,184 @@ merqury:
 genomescope2:
     jobname:    GEP.{rule}.{wildcards.asmID}.{wildcards.kmer}
     memory:     500
-    time:       "00:00:05"
+    time:       "00:05:00"
 
 
 assemblyStats:
     jobname:    GEP.{rule}.{wildcards.asmID}
     memory:     500
-    time:       "00:00:05"
+    time:       "00:05:00"
 
 saveConfiguration_and_getKeyValues_kmer:
     jobname:    GEP.{rule}.{wildcards.asmID}.{wildcards.kmer}
     memory:     500
-    time:       "00:00:05"
+    time:       "00:05:00"
 
 
 saveConfiguration_and_getKeyValues:
     jobname:    GEP.{rule}.{wildcards.asmID}
     memory:     500
-    time:       "00:00:05"
+    time:       "00:05:05"
 
 aggregateAllAssemblies:
     jobname:    GEP.{rule}
     memory:     500
-    time:       "00:00:05"
+    time:       "00:05:05"
 
 
 makeReport:
     jobname:    GEP.{rule}.{wildcards.asmID}.{wildcards.kmer}
     memory:     500
-    time:       "00:00:05"
+    time:       "00:05:05"
 
 
 
 addFullTable:
     jobname:    GEP.{rule}
     memory:     500
-    time:       "00:00:05"
+    time:       "00:05:05"
 
 aggregateReport:
     jobname:    GEP.{rule}
     memory:     500
-    time:       "00:00:05"
+    time:       "00:05:05"
 
 
 makePDF:
     jobname:    GEP.{rule}
     memory:     500
-    time:       "00:00:05"
+    time:       "00:05:05"
+
+###### Rules for illuminadb building ##########
+
+unzipFasta_R1:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trim10x}.{wildcards.trimAdapters}
+    memory:     96000
+    time:       "00:30:05"
+
+
+unzipFasta_R2:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trim10x}.{wildcards.trimAdapters}
+    memory:     96000
+    time:       "00:30:05"
+
+symlinkUnzippedFasta_R1:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trim10x}.{wildcards.trimAdapters}
+    memory:     500
+    time:       "00:00:35"
+
+symlinkUnzippedFasta_R2:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trim10x}.{wildcards.trimAdapters}
+    memory:     500
+    time:       "00:00:35"
+
+
+
+
+symLink_trim10xbarcodes_notrimAdapt:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}
+    memory:     500
+    time:       "00:00:35"
+
+symlinks_no10xOrAdaptTrim:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}
+    memory:     500
+    time:       "00:00:35"
+
+
+symlinks_no10xwithAdaptTrim:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}
+    memory:     500
+    time:       "00:00:35"
+
+
+symlink_trim10xbarcodesR2:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trimAdapters}
+    memory:     500
+    time:       "00:00:35"
+
+
+trim10xbarcodes:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trimAdapters}
+    memory:     500
+    time:       "01:00:05"
+
+
+
+trimAdapters:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trim10x}
+    memory:     500
+    time:       "02:00:05"
+
+
+fastqc_Illumina:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trimAdapters}.{wildcards.trim10x}
+    memory:     500
+    time:       "00:30:05"
+
+multiqc_hifi:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.trimAdapters}.{wildcards.trim10x}
+    memory:     500
+    time:       "00:05:05"
+
+meryl_R1:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trimAdapters}.{wildcards.trim10x}.{wildcards.kmer}
+    memory:     20000
+    time:       "01:00:05"
+
+meryl_R2:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trimAdapters}.{wildcards.trim10x}.{wildcards.kmer}
+    memory:     20000
+    time:       "01:00:05"
+
+meryl_illumina_build:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.trimAdapters}.{wildcards.trim10x}.{wildcards.kmer}
+    memory:     30000
+    time:       "00:45:05"
+
+
+
+
+###### HIFI BUILD #######
+
+unzipHifi:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}
+    memory:     128000
+    time:       "00:30:05"
+
+symlinkUnzippedHifi:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}
+    memory:     500
+    time:       "00:05:05"
+
+symlinkfornotSmartTrimmed:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}
+    memory:     500
+    time:       "00:05:05"
+
+
+fastqc_hifi_SMRT_removed:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}
+    memory:     12000
+    time:       "00:45:05"
+
+multiqc_hifi_SMRTremoved:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}
+    memory:     4000
+    time:       "00:15:05"
+
+meryl_hifi_trimmed_count:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}.{wildcards.kmer}
+    memory:     96000
+    time:       "02:30:05"
+
+meryl_hifi_build:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.smrtornot}.{wildcards.kmer}
+    memory:     96000
+    time:       "01:30:05"
+
+
+trimSMRTbell:
+    jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}
+    memory:     96000
+    time:       "01:30:05"
diff --git a/SUBMIT_CONFIG/slurm/config.yaml b/SUBMIT_CONFIG/slurm/config.yaml
index 07b01f5a0b325352add3c85055df969ada221add..35f16593b733056d061b82d35b185132ef6dfdd6 100644
--- a/SUBMIT_CONFIG/slurm/config.yaml
+++ b/SUBMIT_CONFIG/slurm/config.yaml
@@ -9,9 +9,8 @@ cluster:
     --cpus-per-task={cluster.nCPUs}
     --mem={cluster.memory}
     --job-name={cluster.jobname}
-    --output=slurm_logs/{rule}/{rule}-{wildcards}-%j.out
+    --output=slurm_logs/{rule}/{rule}.{wildcards}.%j.out
     --time={cluster.time}
-    --nodes={cluster.nodes}
 
 #User Defines below parameters
 
diff --git a/rules/hifi_05_11_21.smk b/rules/hifi_05_11_21.smk
index 2648a562c8590bc90ae552c5a2ef17a1bb2d3670..64b27dc00b21a08dce228f9011a37fe172ad6dad 100644
--- a/rules/hifi_05_11_21.smk
+++ b/rules/hifi_05_11_21.smk
@@ -38,9 +38,11 @@ rule unzipHifi:
 		os.path.join(config['Results'], "0_buildDatabases/{sample}/logs/hifiReads/{readCounter}.{smrtornot}_pigzUnzip.log")
 	conda:
 		"../envs/pigz.yaml"
+	threads:
+		4
 	shell:
 		"""
-		pigz -c -d -k {input.fastq} > {output} 2> {log}
+		pigz -p {threads} -c -d -k {input.fastq} > {output} 2> {log}
 		"""
 
 rule symlinkUnzippedHifi:
@@ -50,6 +52,8 @@ rule symlinkUnzippedHifi:
 		os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/01_unzipFastqs/{readCounter}.{smrtornot}.fastq"),
 	log:
 		os.path.join(config['Results'], "0_buildDatabases/{sample}/logs/hifiReads/{readCounter}.{smrtornot}_pigzUnzip.log")
+	threads:
+		1
 	shell:
 		"""
 		ln -s {input.fastq} {output}
@@ -99,6 +103,8 @@ rule symlinkfornotSmartTrimmed:
 		os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/01_unzipFastqs/{readCounter}.notsmrtTrimmed.fastq"),
 	output:
 		outputFile=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/02_trimReads/{readCounter}.notsmrtTrimmed.fastq")
+	threads:
+		1
 	shell:
 		"""
 		ln -s {input} {output.outputFile}
@@ -111,7 +117,8 @@ rule fastqc_hifi_SMRT_removed:
 		folder2out=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/")
 	output:
 		os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/{readCounter}.{smrtornot}_fastqc.html")
-	threads: 1
+	threads:
+		1
 	log:
 		os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{readCounter}.{smrtornot}.FastQC.log")
 	conda:
@@ -130,6 +137,8 @@ rule multiqc_hifi_SMRTremoved:
 		filename="{sample}.{smrtornot}.multiqcReport.html"
 	output:
 		os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/{sample}.{smrtornot}.multiqcReport.html")
+	threads:
+		1
 	log:
 		os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{sample}.{smrtornot}.multiqc.log")
 	conda:
@@ -149,7 +158,7 @@ rule meryl_hifi_trimmed_count:
 		kmer = "{kmer}"
 #		path= os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/")
 	threads:
-		workflow.cores * 0.25
+		16
 	output:
 		directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/03_merylDb/" + "{readCounter}" + "_hifi_dB.{smrtornot}.{kmer}.meryl")),
 	log:
@@ -172,7 +181,7 @@ rule meryl_hifi_build:
 	params:
 		kmer = "{kmer}"
 	threads:
-		workflow.cores * 0.5
+		16
 	output:
 		directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/03_merylDb/complete_hifi_{sample}_dB.{smrtornot}.{kmer}.meryl")),
 	log:
diff --git a/rules/illumina_05_11_21.smk b/rules/illumina_05_11_21.smk
index b8729f913e9f11f4a6eedef4766532d832495813..83fb00ba7be6c583d05705d78a58334e168808aa 100644
--- a/rules/illumina_05_11_21.smk
+++ b/rules/illumina_05_11_21.smk
@@ -45,9 +45,11 @@ rule unzipFasta_R1:
 		os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_R1_pigzUnzip.log")
 	conda:
 		"../envs/pigz.yaml"
+	threads:
+		4
 	shell:
 		"""
-		pigz -c -d -k {input.assembly} > {output} 2> {log}
+		pigz -p {threads} -c -d -k {input.assembly} > {output} 2> {log}
 		"""
 
 rule symlinkUnzippedFasta_R1:
@@ -55,6 +57,8 @@ rule symlinkUnzippedFasta_R1:
 		assembly=R1_notgzipped,
 	output:
 		temp(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R1.fastq")),
+	threads:
+		1
 	shell:
 		"""
 		ln -s {input} {output}
@@ -69,9 +73,11 @@ rule unzipFasta_R2:
 		os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_R2_pigzUnzip.log")
 	conda:
 		"../envs/pigz.yaml"
+	threads:
+		4
 	shell:
 		"""
-		pigz -c -d -k {input.assembly} > {output} 2> {log}
+		pigz -p {threads} -c -d -k {input.assembly} > {output} 2> {log}
 		"""
 
 rule symlinkUnzippedFasta_R2:
@@ -79,6 +85,8 @@ rule symlinkUnzippedFasta_R2:
 		assembly=R2_notgzipped,
 	output:
 		temp(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R2.fastq")),
+	threads:
+		1
 	shell:
 		"""
 		ln -s {input} {output}
@@ -93,7 +101,7 @@ rule trim10xbarcodes:
 		read1=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read1.fastq")),
 #		read2=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read2.fastq"))
 	threads:
-		workflow.cores * 0.125
+		4
 	log:
 		os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.10xTrimmed.10BarcodeRemoval_Trimmomatic.{trimAdapters}.log")
 	conda:
@@ -105,7 +113,7 @@ rule trim10xbarcodes:
 #		ln -s {input.read2} {output.read2}
 
 
-rule trim10xbarcodesR2:
+rule symlink_trim10xbarcodesR2:
 	input:
 		read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.10xTrimmed.{trimAdapters}_R2.fastq")
 	output:
@@ -128,6 +136,8 @@ rule symLink_trim10xbarcodes_notrimAdapt:
 	output:
 		read1=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_val_1.fq")),
 		read2=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_val_2.fq"))
+	threads:
+		1
 	shell:
 		"""
 		ln -s {input.read1} {output.read1}
@@ -141,6 +151,8 @@ rule symlinks_no10xOrAdaptTrim:
 	output:
 		read1=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.not10xTrimmed.notAdaptTrimmed_val_1.fq")),
 		read2=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.not10xTrimmed.notAdaptTrimmed_val_2.fq"))
+	threads:
+		1
 	shell:
 		"""
 		ln -s {input.read1} {output.read1}
@@ -154,6 +166,8 @@ rule symlinks_no10xwithAdaptTrim:
 	output:
 		read1=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.not10xTrimmed.AdaptTrimmed_Read1.fastq")),
 		read2=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.not10xTrimmed.AdaptTrimmed_Read2.fastq"))
+	threads:
+		1
 	shell:
 		"""
 		ln -s {input.read1} {output.read1}
@@ -193,13 +207,14 @@ rule fastqc_Illumina:
 		os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/04_fastqc/{readCounter}.{trim10x}.{trimAdapters}_val_2_fastqc.html")
 	log:
 		os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_fastqc.log")
-	threads: 1
+	threads:
+		4
 	conda:
 		"../envs/pigz.yaml"
 	shell:
 		"(fastqc {input} -o {params.folder2out} -t {threads}) &> {log}"
 
-rule multiqc_hifi_SMRTremoved:
+rule multiqc_hifi:
 	input:
 		read1=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/04_fastqc/{readCounter}.{trim10x}.{trimAdapters}_val_1_fastqc.html"), sample=wildcards.sample, readCounter=d[wildcards.sample], trim10x=testDict[wildcards.sample][1], trimAdapters=testDict[wildcards.sample][2]),
 		read2=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/04_fastqc/{readCounter}.{trim10x}.{trimAdapters}_val_2_fastqc.html"), sample=wildcards.sample, readCounter=d[wildcards.sample], trim10x=testDict[wildcards.sample][1], trimAdapters=testDict[wildcards.sample][2])
@@ -211,6 +226,8 @@ rule multiqc_hifi_SMRTremoved:
 		os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/05_multiqc/{sample}.{trim10x}.{trimAdapters}.multiqcReport.html")
 	log:
 		os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{sample}.{trim10x}.{trimAdapters}_multiqc.log")
+	threads:
+		1
 	conda:
 		"../envs/pigz.yaml"
 	shell:
@@ -225,7 +242,7 @@ rule meryl_R1:
 		kmer = "{kmer}",
 #		path= os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/")
 	threads:
-		workflow.cores * 0.25
+		16
 	output:
 		temp(directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/03_merylDb/{readCounter}.{trim10x}.{trimAdapters}_R1.{kmer}.meryl")))
 	log:
@@ -247,7 +264,7 @@ rule meryl_R2:
 		kmer = "{kmer}",
 #		path= os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/")
 	threads:
-		workflow.cores * 0.25
+		16
 	output:
 		temp(directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/03_merylDb/{readCounter}.{trim10x}.{trimAdapters}_R2.{kmer}.meryl")))
 	log:
@@ -263,7 +280,7 @@ rule meryl_R2:
 		"""
 
 
-rule meryl_hifi_build:
+rule meryl_illumina_build:
 	input:
 #		reads= rules.trimSMRTbell.output.outputFile{readCounter}.{trim10x}.{trimAdapters}
 #		lambda wildcards: expand(config['Results'],"{group}/alignment/{sample}.bam", group=wildcards.group, sample=GROUPS[wildcards.group]
@@ -274,7 +291,7 @@ rule meryl_hifi_build:
 		kmer = "{kmer}",
 		path= os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/03_merylDb/")
 	threads:
-		workflow.cores * 0.5
+		16
 	output:
 		directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/03_merylDb/{sample}_illuminaDb.{trim10x}.{trimAdapters}.{kmer}.meryl")),
 	log:
diff --git a/rules/run_05_11_21.smk b/rules/run_05_11_21.smk
index a0728058afa3fdce087e5acffc8cfd76d8e23fe8..52b80adec54dd6eea7fcbdf05dc1ad4308ae8020 100644
--- a/rules/run_05_11_21.smk
+++ b/rules/run_05_11_21.smk
@@ -111,7 +111,7 @@ rule busco5:
 	shell:
 		"""
 		cd {params.chngDir}
-		(busco -m {params.mode} --in {input.assembly} -o {params.assemblyName} -l {input.lineage} -c {threads} -f --limit 5) &> {log}
+		(busco -m --offline {params.mode} --in {input.assembly} -o {params.assemblyName} -l {input.lineage} -c {threads} -f --limit 5) &> {log}
 		"""
 #		ln -s {input.assembly} {output.symlink}
 
@@ -395,7 +395,7 @@ rule saveConfiguration_and_getKeyValues:
 		echo "$(grep 'total_bps' {input.scaffStats} | awk {{'print $3'}})" >> {params.keyValues}
 		echo "$(grep 'Genome Haploid Length' {input.gscopeSum} | awk {{'print $6'}} )" >> {params.keyValues}
 		echo "$(grep 'Heterozygous (ab)' {input.gscopeSum} | awk {{'print $4'}})" >> {params.keyValues}
-		echo "$(grep 'gc_content' {input.scaffStats} | awk {{'print $2'}})" >> {params.keyValues}
+		echo "$(grep 'gc_content' {input.scaffStats} | awk {{'print $3'}})" >> {params.keyValues}
 		echo "$(grep 'sequence_count' {input.scaffStats} | awk {{'print $2'}})" >> {params.keyValues}
 		echo "$(grep 'sequence_count' {input.contStats} | awk {{'print $2'}})" >> {params.keyValues}
 		echo "$(grep 'number_of_gaps' {input.contStats} | awk {{'print $2'}})" >> {params.keyValues}
diff --git a/scripts/stats.py b/scripts/stats.py
index 38b1fc441a29171a8a83449cdd8eefea741d2a79..a374b702b34e0b3a08b515ede0344ba32663b7cc 100644
--- a/scripts/stats.py
+++ b/scripts/stats.py
@@ -91,6 +91,7 @@ def read_genome(fasta_file):
 				total_len += len(contig)
 				contig_lens.append(len(contig))
 				gc_cont = (gc / total_len) * 100
+#	print("this is gc_content", gc_cont)
 	return contig_lens, scaffold_lens, gc_cont
 
 
@@ -182,10 +183,13 @@ if __name__ == "__main__":
 	contig_lens, scaffold_lens, gc_cont = read_genome(infilename)
 #    contig_stats = calculate_stats(contig_lens, gc_cont)
 	scaffold_stats = calculate_stats(scaffold_lens, gc_cont)
+	rounded_gc = round(gc_cont, 4)
+#	print("this is the rounded_gc: ", rounded_gc)
 	contig_stats = calculate_stats(contig_lens, gc_cont)
 	gaps=contig_stats.get('sequence_count') - scaffold_stats.get('sequence_count')
 	scaffold_stats['number_of_gaps'] = gaps
 	contig_stats['number_of_gaps'] = gaps
+#	print("this is the scaffold_stats: ", scaffold_stats)
 #    print(scaffold_stats)
 #    df_scaffold_all= pd.DataFrame.from_dict(scaffold_stats, orient= 'index')
 #    print(df_scaffold_all)
@@ -196,8 +200,14 @@ if __name__ == "__main__":
 #    s.reset_index()
 #    print(s)
 	scaff_seq=pd.DataFrame(scaffold_stats.items(), columns=['Assembly:', naming])
+#	print("this is the scaff_seq: ", scaff_seq)
 	df_scaffold_top=scaff_seq.iloc[0:7,0:2]
+#	print("this is GC CONTENT", gc_cont)
 	df_scaffold_top[naming]=df_scaffold_top[naming].astype('int64').apply('{:,}'.format)
+#	print("this is the top: ", df_scaffold_top)
+	df_scaffold_top[naming][2] = rounded_gc
+#	print("this is df_scaffold_top[naming][2]", df_scaffold_top[naming][2])
+#	print("this is the top: ", df_scaffold_top)
     # df_scaffold_top=df_scaffold_top.style.hide_index()
 #    df_scaffold_top[naming].round(decimals=0)
     # df_contig_all=pd.DataFrame(data=contig_stats)
@@ -232,6 +242,7 @@ if __name__ == "__main__":
 	contig_seq=pd.DataFrame(contig_stats.items(), columns=['Assembly:', naming])
 	df_contig_top=contig_seq.iloc[0:7,0:2]
 	df_contig_top[naming]=df_contig_top[naming].astype('int64').apply('{:,}'.format)
+	df_contig_top[naming][2] = rounded_gc
     # df_scaffold_top=df_scaffold_top.style.hide_index()
 #    df_scaffold_top[naming].round(decimals=0)
     # df_contig_all=pd.DataFrame(data=contig_stats)
@@ -326,21 +337,21 @@ if __name__ == "__main__":
     #      print(tabulate(df_contig_L_LG, headers='keys',tablefmt="rst", showindex=False), file=outputRst2)
     #      print("", file=outputRst2)
 
-	with open(sys.argv[4], 'w') as outputRst:
-		print(tabulate(df_scaffold_top, headers='keys',tablefmt="pipe", showindex=False), file=outputRst)
-		print("", file=outputRst)
-		print(tabulate(df_scaffold_N_NG, headers='keys',tablefmt="pipe", showindex=False), file=outputRst)
-		print("", file=outputRst)
-		print(tabulate(df_scaffold_L_LG, headers='keys',tablefmt="pipe", showindex=False), file=outputRst)
-		print("", file=outputRst)
-	#
-	with open(sys.argv[5], 'w') as outputRst2:
-		print(tabulate(df_contig_top, headers='keys',tablefmt="pipe", showindex=False), file=outputRst2)
-		print("", file=outputRst2)
-		print(tabulate(df_contig_N_NG, headers='keys',tablefmt="pipe", showindex=False), file=outputRst2)
-		print("", file=outputRst2)
-		print(tabulate(df_contig_L_LG, headers='keys',tablefmt="pipe", showindex=False), file=outputRst2)
-		print("", file=outputRst2)
+	# with open(sys.argv[4], 'w') as outputRst:
+	# 	print(tabulate(df_scaffold_top, headers='keys',tablefmt="pipe", showindex=False), file=outputRst)
+	# 	print("", file=outputRst)
+	# 	print(tabulate(df_scaffold_N_NG, headers='keys',tablefmt="pipe", showindex=False), file=outputRst)
+	# 	print("", file=outputRst)
+	# 	print(tabulate(df_scaffold_L_LG, headers='keys',tablefmt="pipe", showindex=False), file=outputRst)
+	# 	print("", file=outputRst)
+	# #
+	# with open(sys.argv[5], 'w') as outputRst2:
+	# 	print(tabulate(df_contig_top, headers='keys',tablefmt="pipe", showindex=False), file=outputRst2)
+	# 	print("", file=outputRst2)
+	# 	print(tabulate(df_contig_N_NG, headers='keys',tablefmt="pipe", showindex=False), file=outputRst2)
+	# 	print("", file=outputRst2)
+	# 	print(tabulate(df_contig_L_LG, headers='keys',tablefmt="pipe", showindex=False), file=outputRst2)
+	# 	print("", file=outputRst2)
 	# list_of_dfs=[df_scaffold_top,df_scaffold_N_NG,df_scaffold_L_LG]
     # for df in list_of_dfs:
     #     with open('all_dfs.tsv','a') as f: