From 1599f79114e4a67b42cf8d2c15769ae041d31b3b Mon Sep 17 00:00:00 2001 From: ytirlet <101868688+ytirlet@users.noreply.github.com> Date: Fri, 14 Apr 2023 14:18:13 +0200 Subject: [PATCH] Update pipeline.py --- pipeline.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipeline.py b/pipeline.py index 56dd6e0..aa1af3e 100644 --- a/pipeline.py +++ b/pipeline.py @@ -130,7 +130,7 @@ def main() : gff = output_path + name + '/' + name + '.emapper.genepred.gff' annot = output_path + name + '/' + name + '.emapper.annotations' out_file = output_path + name + '/' + name + '.gbk' - os.system('emapper2gbk genomes -fn ' + genom + ' -fp ' + prot + ' -g ' + gff + ' -a ' + annot + ' -o ' + out_file + ' -gt eggnog -c 5') + os.system('emapper2gbk genomes -fn ' + genom + ' -fp ' + prot + ' -g ' + gff + ' -a ' + annot + ' -o ' + out_file + ' -gt eggnog -c 40') else : raise ValueError("The specified annotation tool is not recognized. Please retry with 'eggnog' or 'prokka'. Default is 'prokka'.")