job set to 1 for local run, -j will be used only for --sge

metaclade2

@@ -35,8 +35,8 @@ MCLADE_USESGE=false
 MCLADE_WORKDIR=${PWD}
 MCLADE_OUTFILE=""
 MCLADE_RMTMP=false
-NTHREADS=1
-NJOBS=16
+NTHREADS=4
+NJOBS=1
 
 function print_usage() {
     echo -en "\n  USAGE: ${CMD_NAME} -i <input_fasta> -N <name> [options]\n"
@@ -71,13 +71,14 @@ function print_usage() {
     " | column -t -s $'\t'
     echo -en "\n"
     echo -en "  OTHER OPTIONS:\n
-    -j, --jobs <num>\tNumber of jobs to be created (default:${NJOBS})\n
-    -t, --threads <num>\tNumber of threads for each job (default:${NTHREADS})\n
+    -t, --threads <num>\tNumber of threads (default:${NTHREADS})\n
     -h, --help\tPrint this help message\n
     -V, --version\tPrint version\n" | column -t -s $'\t'
     echo -en "\n"
     echo -en "  SGE OPTIONS:\n
     --sge\tRun MetaCLADE jobs on a SGE HPC environment\n
+    -j, --jobs <num>\tNumber of jobs to be created/submitted (default:${NJOBS})\n
+                    \tUse -t|--threads to define the number of threads for each job\n
     --pe <name>\tParallel environment to use (mandatory)\n
     --queue <name>\tName of a specific queue where jobs are submitted\n
     --time-limit <hh:mm:ss>\tTime limit for submitted jobs formatted as hh:mm:ss\n
@@ -231,7 +232,7 @@ if ! [[ "${NTHREADS}" =~ ^[0-9]+$ ]] || [ ${NTHREADS} -lt 1 ] ; then
 fi
 
 if ! [[ "${NJOBS}" =~ ^[0-9]+$ ]] || [ ${NJOBS} -lt 1 ] ; then
-    print_warning "-j|--max-jobs parameter should be a positive integer"
+    print_error "-j|--max-jobs parameter should be a positive integer"
     exit 1
 fi
 
@@ -251,6 +252,9 @@ if [ "${MCLADE_USESGE}" = true ] ; then
     fi
 fi
 
+# set number of job to 1 if run on a single computer
+if [ "${MCLADE_USESGE}" = false ]; then NJOBS=1; fi
+
 # Create Working directory
 MCLADE_WORKDIR=${MCLADE_WORKDIR}"/"${MCLADE_JOBNAME}
 mkdir -p "${MCLADE_WORKDIR}" "${MCLADE_WORKDIR}/log"