Added more checks for the sbatch version (scratch folder existence, number of...

Added more checks for the sbatch version (scratch folder existence, number of threads for the main script)

wGRR

@@ -7,7 +7,7 @@ trap 'rm -rf "$tmp"' EXIT
 export LC_ALL=C
 SECONDS=0
 
-readonly VERSION=1.4
+readonly VERSION=1.4.1
 
 bold=$(tput bold)
 green=$(tput setaf 2)
@@ -136,7 +136,7 @@ while getopts :fTsji:p:o:t:a:m:l:C:I: option ; do
    case $option in
    i) PRT="$OPTARG";       if [[ ! -s $PRT ]]; then printf "${bold}${red}%-17s  --  %s\n${normal}"  "[ERROR]" "Fasta file '$PRT' not found or empty (option -i)." ; exit 1 ; fi ;;
    p) MMPATH="$OPTARG"          ;;
-   o) OUT="$OPTARG";       if [[ -f "$OUT".wgrr.final.txt ]]; then printf "${bold}${red}%-17s  --  %s\n${normal}"  "[ERROR]" "File $OUT.wgrr.final.txt already exists. Change option -o or remove this file and relaunch." ; exit 1 ; fi ;;
+   o) OUT="$OPTARG";       if [[ -f "$OUT".wgrr.final.txt ]]; then printf "${bold}${red}%-17s  --  %s\n${normal}"  "[ERROR]" "File $OUT.wgrr.final.txt already exists. Change option -o or remove this file and relaunch." ; exit 1 ; elif [[ ${OUT} =~ / ]] ; then printf "${bold}${red}%-17s  --  %s\n${normal}"  "[ERROR]" "You cannot use a path as a prefix with -o option. Please use a simple string instead." ; exit 1 ; fi ;;
 	t) THREADS="$OPTARG";   if [[ ! $THREADS =~ ^[0-9]+$ ]]; then printf "${bold}${red}%-17s  --  %s\n${normal}"  "[ERROR]" "Number of threads $THREADS must be an integer (option -t)." ; exit 1 ; fi ;;
 	a) ARRAYSIZE="$OPTARG"; if [[ ! $ARRAYSIZE =~ ^[0-9]+$ ]]; then if [[ $ARRAYSIZE != "AUTO" ]] ; then printf "${bold}${red}%-17s  --  %s\n${normal}" "[ERROR]" "Number of genomes comparisons $ARRAYSIZE must be an integer (option -a)." ; exit 1 ; fi ; fi ;;
 	l) IDLIST="$OPTARG";    if [[ ! -s ${IDLIST} ]] ; then printf "${bold}${red}%-17s  --  %s\n${normal}" "[ERROR]" "File ${IDLIST} not found or empty (option -l)." ; exit 1 ; fi ;;
@@ -180,7 +180,10 @@ if [[ $? -eq 1 ]] ; then
 	tmp=$(mktemp -d tmp-XXXXXX)
 else
 	if [[ `hostname` == "maestro-"* ]] ; then
-		tmp=$(mktemp -p $MYSCRATCH -d tmp-XXXXXXXX)
+		if [[ ! -d ${APPASCRATCH}/${USER} ]] ; then
+			mkdir ${APPASCRATCH}/${USER}
+		fi
+		tmp=$(mktemp -p ${APPASCRATCH}/${USER} -d tmp-XXXXXXXX)
 	else
 		tmp=$(mktemp -d tmp-XXXXXXXX)
 	fi
@@ -198,7 +201,7 @@ fi
 
 # Get system total memory if not in sbatch
 TOTALMEM=0
-if [[ $BATCHFLAG==0 ]] ; then
+if [[ $BATCHFLAG == 0 ]] ; then
 	if [[ $SLURM_JOBID != "" ]] ; then
 		TOTALMEM=$(sacct -j $SLURM_JOBID -o ReqMem | awk 'NR==3{print $1;exit}' | numfmt --from=iec)
 	else
@@ -212,6 +215,9 @@ if [[ $BATCHFLAG==0 ]] ; then
 			fi
 		fi
 	fi
+elif [[ $(nproc) -gt 1 ]] ; then
+	printf "${bold}${yellow}%-17s  --  %s\n${normal}" "[WARNING]" "You requested $(nproc) threads (sbatch -c $(nproc)) but wGRR main script will use only one in sbatch mode."  | tee -a ${OUT}.wgrr.log
+	printf "${bold}${yellow}%-17s  --  %s\n${normal}" "[WARNING]" "You should not use the -c option of sbatch when running wGRR this way."  | tee -a ${OUT}.wgrr.log
 fi
 
 printf "%-17s  --  %s\n" "["$(textifyDuration $SECONDS)"]" "wGRR version ${VERSION}" | tee -a ${OUT}.wgrr.log