LOGS

.gitignore

-.log/
+LOGS/
 .snakemake/
 DATA/
 work/
 report/
+.Rproj.user
+.Rhistory

DADA2.Rproj

+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX

RunSnake.sh

@@ -3,7 +3,7 @@ export PYTHONPATH=''
 source /usr/local/genome/Anaconda2-5.1.0/etc/profile.d/conda.sh
 conda activate snakemake-5.7.4
 
-mkdir -p ./.log/out/ ./.log/err/
+mkdir -p LOGS/
 
 snakemake \
 --snakefile $1 \

cluster.json

 {
 	"__default__" :
 	{
-		"out" : "./.log/out/",
-		"err" : "./.log/err/",
-		"queue" : "short.q",
+		"out" : "LOGS/",
+		"err" : "LOGS/",
+		"queue" : "maiage.q",
 		"cluster" : ""
 	}
 }

global.smk

@@ -15,7 +15,8 @@ rule all:
 		"report/clusters_metrics.html",
 		"report/affiliations_metrics.html",
 		"report/abundance.biom",
-		"report/abundance.tsv"
+		"report/abundance.tsv",
+		"report/tree.nwk"
 
 include: "quality.smk"
 include: "preprocess.smk"

qsubSnake.sh

-mkdir -p ./.log/out/ ./.log/err/
-qsub -V -cwd -o ./.log/out/ -e ./.log/err/ -q maiage.q,long.q -N `basename $1` RunSnake.sh $1
+mkdir -p LOGS/
+qsub -V -cwd -o LOGS/ -e LOGS/ -q maiage.q,long.q -N `basename $1` RunSnake.sh $1