From 5c79ec36434fc92a897d0c22b1b969bf3dd11d4c Mon Sep 17 00:00:00 2001 From: sepro Date: Tue, 14 Jun 2016 14:50:47 +0200 Subject: [PATCH] bugfix --- pipeline/orthology.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pipeline/orthology.py b/pipeline/orthology.py index 46d384d..0d86eb7 100644 --- a/pipeline/orthology.py +++ b/pipeline/orthology.py @@ -16,7 +16,7 @@ def run_orthofinder(self): orthofinder_dir = self.dp['GLOBAL']['orthofinder_output'] orthofinder_cores = self.cp['TOOLS']['orthofinder_cores'] - os.makedirs(os.path.dirname(orthofinder_dir), exist_ok=True) + os.makedirs(orthofinder_dir, exist_ok=True) filename, jobname = self.write_submission_script("orthofinder_%d", self.python_module + ' ' + @@ -26,6 +26,7 @@ def run_orthofinder(self): "orthofinder_%d.sh") for g in self.genomes: + print('çopying', self.dp[g]['protein_fasta'], 'to', os.path.join(orthofinder_dir, g + '.fasta')) copy(self.dp[g]['protein_fasta'], os.path.join(orthofinder_dir, g + '.fasta')) subprocess.call(["qsub", "-pe", "cores", orthofinder_cores, "-v", "fasta_dir=" + orthofinder_dir + ",num_cores=" + orthofinder_cores, filename])