diff --git a/prepare_annotation/.gitignore b/prepare_annotation/.gitignore
index 6409a943f2cb808a200abc44897efa1e9d66cd54..06cd4097a1ab378199d07c82a5014afbff8d30d0 100644
--- a/prepare_annotation/.gitignore
+++ b/prepare_annotation/.gitignore
@@ -3,3 +3,4 @@ Log.out
 results
 logs
 dag.png
+nohup.out
diff --git a/prepare_annotation/Snakefile b/prepare_annotation/Snakefile
index 2916eaefacc8056af717abea50e176f6bb331ea1..efd220e2be5a71ef5963af80034fda9cce6af1ca 100644
--- a/prepare_annotation/Snakefile
+++ b/prepare_annotation/Snakefile
@@ -125,16 +125,15 @@ rule index_genome_STAR:
 	log:
 		os.path.join(config["local_log"],"index_genome_STAR.log")
 	shell:
-		"(mkdir -p {output.output}; \
+		"mkdir -p {output.output}; \
 		chmod -R 777 {output.output}; \
-		STAR --runMode genomeGenerate \
+		(STAR --runMode genomeGenerate \
 		--sjdbOverhang {params.sjdbOverhang} \
 		--genomeDir {params.outputdir} \
 		--genomeFastaFiles {input.genome} \
 		--runThreadN {threads} \
 		--sjdbGTFfile {input.annotation}) &> {log}"
 
-
 ##################################################################################
 ### Filter protein coding and lncRNA transcripts
 ##################################################################################
@@ -197,4 +196,4 @@ rule index_salmon:
 		--transcripts {input.transcripts} \
 		--index {output.index} \
 		--kmerLen {params.kmerLen} \
-		--threads {threads}) > {log}"
+		--threads {threads}) &> {log}"
diff --git a/prepare_annotation/cluster.json b/prepare_annotation/cluster.json
index 9ac8511c1851f70d6b491a9e57bfa23c0399c980..a6bfdd5fa4aea8da21bdaff8c6f0d0ad96c1c6d8 100644
--- a/prepare_annotation/cluster.json
+++ b/prepare_annotation/cluster.json
@@ -18,6 +18,6 @@
   {
     "time": "06:00:00",
     "threads":"8",
-    "mem":"50G"
+    "mem":"75G"
   }
 }
diff --git a/prepare_annotation/config.yaml b/prepare_annotation/config.yaml
index 00b9a5d2c233971bace551d9b54742ac9dcf1aa3..92249c924ed5882411b3eb5c031bc74c733b6261 100644
--- a/prepare_annotation/config.yaml
+++ b/prepare_annotation/config.yaml
@@ -3,7 +3,30 @@
   ### Annotation
   ##############################################################################
   genome: ["ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.1.fa.gz",
-           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.2.fa.gz"]
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.2.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.3.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.4.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.5.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.6.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.7.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.8.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.9.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.10.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.11.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.12.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.13.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.14.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.15.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.16.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.17.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.18.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.19.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.20.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.21.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.22.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.X.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.Y.fa.gz",
+           "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.MT.fa.gz"]
   annotation: ["ftp://ftp.ensembl.org/pub/release-89/gtf/homo_sapiens/Homo_sapiens.GRCh38.89.chr.gtf.gz"]
   other_RNA: "other.fa"
   ##############################################################################