diff --git a/rules/init.skm b/rules/init.skm
index 688ff4b..6f4ee1d 100644
--- a/rules/init.skm
+++ b/rules/init.skm
@@ -51,6 +51,7 @@ if os.path.isfile('./NCBI_accession_list.txt'):
                 download_file.write( "numLines=$(fastq-dump.2.9.1 -X 1 -Z --split-spot $srr | wc -l)" + "\n")
                 download_file.write( "if [ $numLines -eq 8 ]; then cat FASTQ/${srr}_1.fastq FASTQ/${srr}_2.fastq > FASTQ/$srr.fastq && rm FASTQ/${srr}_1.fastq FASTQ/${srr}_2.fastq; fi"  + "\n")
                 download_file.write( "if [ -f FASTQ/${srr}_1.fastq ]; then mv FASTQ/${srr}_1.fastq FASTQ/${srr}.fastq ; elif [ -f FASTQ/${srr}_2.fastq ]; then mv FASTQ/${srr}_2.fastq FASTQ/${srr}.fastq; fi"  + "\n")
+                download_file.write( "gzip FASTQ/${srr}.fastq" + "\n")   #gzip output
 
 
 if os.path.isfile("./local_samples.tsv"):