diff --git a/rules/rulesNew.smk b/rules/rulesNew.smk
index b7835de48507a3dabe5a998076686c7941086b60..c94a9cb6f394c4ad82e1f1b6a3514a9b0dccbdff 100644
--- a/rules/rulesNew.smk
+++ b/rules/rulesNew.smk
@@ -146,7 +146,8 @@ rule meryl_R1:
 		read1= rules.combine_illuminaReads_R1.output
 #		check = os.path.join(config['Results'], "{sample}" + "/busco5/short_summary.specific." + config['busco5Lineage'] + "_odb10." + "{sample}" + ".txt")
 	params:
-		script = os.path.join(workflow.basedir, "programs/meryl/*/bin/meryl"),
+#		script = os.path.join(workflow.basedir, "programs/meryl/build/bin/meryl"),
+		script = os.path.join(workflow.basedir, "programs/meryl-1.0/Linux-amd64/bin/meryl"),
 		kmer = 21,
 		r1= "{sample}" + "_R1.21.meryl",
 		path= os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/")
@@ -170,7 +171,8 @@ rule meryl_R2:
 		read2= rules.combine_illuminaReads_R2.output
 #		check = os.path.join(config['Results'], "{sample}" + "/busco5/short_summary.specific." + config['busco5Lineage'] + "_odb10." + "{sample}" + ".txt")
 	params:
-		script = os.path.join(workflow.basedir, "programs/meryl/*/bin/meryl"),
+#		script = os.path.join(workflow.basedir, "programs/meryl/build/bin/meryl"),
+		script = os.path.join(workflow.basedir, "programs/meryl-1.0/Linux-amd64/bin/meryl"),
 		kmer = 21,
 		r2= "{sample}" + "_R2.21.meryl",
 		path= os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/")
@@ -195,7 +197,8 @@ rule meryl:
 		read2=os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/" + "{sample}" + "_R2.21.meryl")
 #		check = os.path.join(config['Results'], "{sample}" + "/busco5/short_summary.specific." + config['busco5Lineage'] + "_odb10." + "{sample}" + ".txt")
 	params:
-		script = os.path.join(workflow.basedir, "programs/meryl/*/bin/meryl"),
+#		script = os.path.join(workflow.basedir, "programs/meryl/build/bin/meryl"),
+		script = os.path.join(workflow.basedir, "programs/meryl-1.0/Linux-amd64/bin/meryl"),
 		kmer = 21,
 #		r1= "{sample}" + "_R1.21.meryl",
 #		r2= "{sample}" + "_R2.21.meryl",
@@ -226,17 +229,18 @@ rule merqury:
 		script = os.path.join(workflow.basedir, "programs/merqury-1.1/merqury.sh"),
 		outFile= "{sample}" + "_merq",
 #		outFile= os.path.join(config['Results'], "{sample}" +"/QVstats_merylAndMerqury/{sample}_merq"),
-		merylPath = os.path.join(workflow.basedir, "programs/meryl/*/bin:$PATH"),
+#		merylPath = os.path.join(workflow.basedir, "programs/meryl/build/bin:$PATH"),
+		merylPath = os.path.join(workflow.basedir, "programs/meryl-1.0/Linux-amd64/bin:$PATH"),
 		outPath= os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury"),
 		export= os.path.join(workflow.basedir, "programs/merqury-1.1")
-		# symlink=os.path.join(config['Results'], "{sample}" + "/{sample}.fasta")
 	threads:
 		workflow.cores * 0.5
 	output:
 		report(os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.qv"), caption="../report/merqury/qvScore.rst", category="QV Estimate", subcategory="{sample}"),
-		report(os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.st.png"), caption="../report/merqury/spectra-cn_stacked.rst", category="Copy Number Spectra Plots", subcategory="{sample}"),
-		report(os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.fl.png"), caption="../report/merqury/spectra-cn_filled.rst", category="Copy Number Spectra Plots", subcategory="{sample}"),
-		os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/" + "{sample}" + "_dB.21.hist")
+		report(os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}.spectra-cn.st.png"), caption="../report/merqury/spectra-cn_stacked.rst", category="Copy Number Spectra Plots", subcategory="{sample}"),
+		report(os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}.spectra-cn.fl.png"), caption="../report/merqury/spectra-cn_filled.rst", category="Copy Number Spectra Plots", subcategory="{sample}"),
+		os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/" + "{sample}" + "_dB.21.hist"),
+		symlink=os.path.join(config['Results'], "{sample}" + "/{sample}.fasta")
 	log:
 		os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/logs/{sample}_merqury.log")
 	priority:
@@ -246,10 +250,11 @@ rule merqury:
 	shell:
 		"""
 		cd {params.outPath}
+		ln -s {input.assembly} {output.symlink}
 		export PATH={params.merylPath}
 		export MERQURY={params.export}
 		export OMP_NUM_THREADS={threads}
-		(bash {params.script} {input.merylDB} {input.assembly} {params.outFile}) &> {log}
+		(bash {params.script} {input.merylDB} {output.symlink} {params.outFile}) &> {log}
 		"""
 #				bash {params.script} {input.merylDB} {params.symlink} {params.outFile}
 
@@ -263,11 +268,12 @@ rule merqury:
 rule genomescope2:
 	input:
 		hist=os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/" + "{sample}" + "_dB.21.hist"),
-		check1=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.fl.png"),
-		check2=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.st.png")
+		check1=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}.spectra-cn.fl.png"),
+		check2=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}.spectra-cn.st.png")
 	params:
 		outFolder=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/"),
-		cpHist=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_dB.21.histo")
+		cpHist=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_dB.21.histo"),
+		findGscope=os.path.join(workflow.basedir)
 	output:
 		summary=report(os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_summary.txt"), caption="../report/genomescope/summary.rst", category="Genomescope Profile", subcategory="{sample}"),
 		logPlot=report(os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_log_plot.png"), caption="../report/genomescope/logplot.rst", category="Genomescope Profile", subcategory="{sample}"),
@@ -278,7 +284,8 @@ rule genomescope2:
 	shell:
 		"""
 		expand -t 1 {input.hist} > {params.cpHist}
-		Rscript genomescope2 -i {params.cpHist} -o {params.outFolder} -k 21 -n {wildcards.sample}
+		export genomescope2script=$(find {params.findGscope} -name genomescope2)
+		Rscript $genomescope2script -i {params.cpHist} -o {params.outFolder} -k 21 -n {wildcards.sample}
 		grep "Genome Haploid Length" {output.summary} | awk {{'print $6'}} | sed 's/,//g'> {output.estimatedSize}
 		"""
 
@@ -342,8 +349,8 @@ rule saveConfiguration_and_getKeyValues:
 		gscopeLin=os.path.join(config['Results'], "{sample}" +"/3_genomescopeProfile/" + "{sample}" + "_linear_plot.png"),
 		busco=os.path.join(config['Results'], "{sample}" + "/1_busco5/short_summary.specific." + buscoDataBaseName + "_odb10." + "{sample}" + ".txt"),
 		qv=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.qv"),
-		spectraStacked=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.st.png"),
-		spectraFlat=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.fl.png"),
+		spectraStacked=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}.spectra-cn.st.png"),
+		spectraFlat=os.path.join(config['Results'],"{sample}" + "/2_QVstats_merylAndMerqury/" + "{sample}" + "_merq.{sample}.spectra-cn.fl.png"),
 #		os.path.join(config['Results'],"{sample}" + "/QVstats_merylAndMerqury/logs/" + "{sample}" + "_merqury.log"),
 #		os.path.join(config['Results'],"{sample}" + "/assemblyStats/{sample}_contig_stats.tsv"),
 		scaffStats=os.path.join(config['Results'],"{sample}" + "/4_assemblyStats/{sample}_scaffold_stats.tsv"),
@@ -367,8 +374,8 @@ rule saveConfiguration_and_getKeyValues:
 		gscopeLin=os.path.join(config['Results'], "{sample}" +"/5_Key_Results/" + "{sample}" + "_gScope_linear_plot.png"),
 		busco=os.path.join(config['Results'], "{sample}" + "/5_Key_Results/short_summary.specific." + buscoDataBaseName + "_odb10." + "{sample}" + ".txt"),
 		qv=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/" + "{sample}" + "_merq.qv"),
-		spectraStacked=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.st.png"),
-		spectraFlat=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/" + "{sample}" + "_merq.{sample}_assembly.spectra-cn.fl.png"),
+		spectraStacked=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/" + "{sample}" + "_merq.{sample}.spectra-cn.st.png"),
+		spectraFlat=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/" + "{sample}" + "_merq.{sample}.spectra-cn.fl.png"),
 #		os.path.join(config['Results'],"{sample}" + "/QVstats_merylAndMerqury/logs/" + "{sample}" + "_merqury.log"),
 #		os.path.join(config['Results'],"{sample}" + "/assemblyStats/{sample}_contig_stats.tsv"),
 		scaffStats=os.path.join(config['Results'],"{sample}" + "/5_Key_Results/{sample}_scaffold_stats.tsv"),