Remove unessesary rm command duplicate

FOI-Bioinformatics · Nov 9, 2020 · 6d872e1 · 6d872e1
1 parent 73e84d8
commit 6d872e1
Showing 1 changed file with 5 additions and 2 deletions.
diff --git a/flextaxd/modules/CreateKrakenDatabase.py b/flextaxd/modules/CreateKrakenDatabase.py
@@ -217,11 +217,14 @@ def create_database(self,outdir,keep=False):
 		logger.info("cp {outdir}/*.map {krakendb}".format(outdir=outdir,krakendb=self.krakendb))
 		logger.info(self.krakenversion+"-build --build --db {krakendb} {params} --threads {threads}".format(krakendb=self.krakendb, threads=self.build_processes, params=self.params))
 		os.system(self.krakenversion+"-build --build --skip-maps --db {krakendb} {params} --threads {threads}".format(krakendb=self.krakendb, threads=self.build_processes, params=self.params))
+
 		if self.krakenversion in ["kraken2"]:
 			logger.info("Create inspect file!")
 			os.system(self.krakenversion+"-inspect --db {krakendb} --report-zero-counts --threads {threads} > {krakendb}/inspect.txt".format(krakendb=self.krakendb,threads=self.build_processes ))
+			os.system("gzip {krakendb}/*.map".format(krakendb=self.krakendb))
+			os.system("gzip {krakendb}/inspect.txt".format(krakendb=self.krakendb))
 		if not keep:
 			os.system(self.krakenversion+"-build --clean --db {krakendb}".format(outdir=outdir,krakendb=self.krakendb, threads=self.processes))
-			logger.info("Cleaning up tmp files")
-			os.system('find {krakendb} -maxdepth 1 -name "*.f*a" -print0 | xargs -0 rm'.format(krakendb=self.krakendb))
+			# logger.info("Cleaning up tmp files")
+			# os.system('find {krakendb} -maxdepth 1 -name "*.f*a" -print0 | xargs -0 rm'.format(krakendb=self.krakendb))
 		logger.info("{krakenversion} database created".format(krakenversion=self.krakenversion))