diff --git a/tools/flye/flye.rule.snakefile b/tools/flye/flye.rule.snakefile
index d57d5538bf2b1aa76f7f17b309c458f57fa5d3bc..3f6d9848c3a7ed1703afd957fdf7c8acf6e7f72a 100755
--- a/tools/flye/flye.rule.snakefile
+++ b/tools/flye/flye.rule.snakefile
@@ -20,5 +20,6 @@ rule <step_name>__flye:
         "--out-dir {params.output_dir} "
         "-t {threads} "
         "{params.scaffold} {params.keep_haplotypes} |& tee {log} ;"
-        "awk '/^>/ {{printf(\"\n%s\n\",$0);next; }} {{ printf(\"%s\",$0);}}  END {{printf(\"\n\");}}' < {params.output_dir}/assembly.fasta > {params.output_dir}/assembly.fa; "
-        "mv {params.output_dir}/assembly.fa > {params.output_dir}/assembly.fasta"
\ No newline at end of file
+        "awk '/^>/ {{printf(\"\\n%s\\n\",$0);next; }} {{ printf(\"%s\",$0);}}  END {{printf(\"\\n\");}}' < {params.output_dir}/assembly.fasta > {params.output_dir}/assembly.fa; "
+        "tail -n +2 {params.output_dir}/assembly.fa > {params.output_dir}/assembly.fasta; "
+        "rm -f {params.output_dir}/assembly.fa"
\ No newline at end of file