diff --git a/wGRR b/wGRR
index 02c7a5d0314869f19c1f0a762b14eeaeefb8f4c5..03c6101a62f99ef8c0d371150ed680cc4068bbb7 100755
--- a/wGRR
+++ b/wGRR
@@ -7,7 +7,7 @@ trap 'rm -rf "$tmp"' EXIT
export LC_ALL=C
SECONDS=0
-readonly VERSION=1.4.1
+readonly VERSION=1.4.2
bold=$(tput bold)
green=$(tput setaf 2)
@@ -66,6 +66,8 @@ display_usage() {
echo " -f In sbatch mode, will use the fast QOS (jobs limited to 2 hours)"
echo " ${bold}WARNING:${normal}: be sure the jobs will run under 2 hours otherwise they will fail."
echo " default: off"
+ echo " -n If turned on, the MMseqs output file will be erased to save disk space."
+ echo " default: off"
echo ""
echo "${bold}DESCRIPTION:${normal}"
echo "This pipeline will do all proteins pairwise comparisons using the MMseqs2 software and then process "
@@ -121,18 +123,22 @@ IDLIST="N.O.L.I.S.T" ## -l
BATCHFLAG=0 ## Are we in a sbatch job?
QT=0 ## Queing time (for Maestro)
MAXJOBS=0 ## -m
-MMS_DEF_MAX_SEQS=300
-MIDENT=0
-MMS_MAX_SEQ_PARAM=""
TESTRUN=0 ## -T
FAST=0 ## -f
SKIP=0 ## -s
JACCARD=0 ## -j
COVT=0.5 ## -C
IDT=0.35 ## -I
+NOM8=0 ## -n
+
+MMS_DEF_MAX_SEQS=300
+MIDENT=0
+MMS_MAX_SEQ_PARAM=""
+EST_M8_SIZE=0
+tmp="wgrrtmp"
## catch option values
-while getopts :fTsji:p:o:t:a:m:l:C:I: option ; do
+while getopts :fTsji:p:o:t:a:m:l:C:I:c:n: 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" ;;
@@ -145,6 +151,7 @@ while getopts :fTsji:p:o:t:a:m:l:C:I: option ; do
f) FAST=1 ;;
s) SKIP=1 ;;
j) JACCARD=1 ;;
+ n) NOM8=1 ;;
C) COVT="$OPTARG"; if [[ ${COVT} -gt 1 ]] || [[ ${COVT} -lt 0 ]] ; then printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "Coverage threshold must be between 0 and 1 (option -C)." ; exit 1 ; fi ;;
I) IDT="$OPTARG"; if [[ ${IDT} -gt 1 ]] || [[ ${IDT} -lt 0 ]] ; then printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "Identity threshold must be between 0 and 1 (option -C)." ; exit 1 ; fi ;;
:) printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "option $OPTARG : missing argument" ; exit 1 ;;
@@ -153,6 +160,11 @@ while getopts :fTsji:p:o:t:a:m:l:C:I: option ; do
done
shift "$((OPTIND - 1))"
+if [[ ${PRT} == "N.O.P.R.T" ]] ; then
+ printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "No input file provided (option -i)." | tee -a ${OUT}.wgrr.log
+ exit 1
+fi
+
# Improvement: test if $PRT is a proper fasta file
# Remove all aliases
@@ -177,20 +189,29 @@ fi
/usr/bin/mktemp --version > /dev/null 2>&1
if [[ $? -eq 1 ]] ; then
- tmp=$(mktemp -d tmp-XXXXXX)
+ tmp=$(mktemp -d wgrrtmp-XXXXXX)
else
if [[ `hostname` == "maestro-"* ]] ; then
if [[ ! -d ${APPASCRATCH}/${USER} ]] ; then
mkdir ${APPASCRATCH}/${USER}
fi
- tmp=$(mktemp -p ${APPASCRATCH}/${USER} -d tmp-XXXXXXXX)
+ tmp=$(mktemp -p ${APPASCRATCH}/${USER} -d wgrrtmp-XXXXXXXX)
+ else
+ tmp=$(mktemp -d wgrrtmp-XXXXXXXX)
+ fi
+fi
+
+if [[ ${tmp} == "wgrrtmp" ]] ; then
+ if [[ -d ${tmp} ]] ; then
+ printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "Could not create temporary directory. Please delete ${tmp} directory and relaunch the analysis." | tee -a ${OUT}.wgrr.log
+ exit 1
else
- tmp=$(mktemp -d tmp-XXXXXXXX)
+ mkdir ${tmp}
fi
fi
if [[ $OUT == "N.O.O.U.T" ]] ; then
- OUT=$(basename $tmp)
+ OUT=$(basename $tmp | cut -d'-' -f 2)
fi
## Get partition (if sbatch) or check nproc (if local/Check number of threads
@@ -222,6 +243,18 @@ fi
printf "%-17s -- %s\n" "["$(textifyDuration $SECONDS)"]" "wGRR version ${VERSION}" | tee -a ${OUT}.wgrr.log
+NTMP=0
+for f in ${tmp}/../wgrrtmp* ; do
+ if [[ -d ${f} ]] ; then
+ NTMP=$(( NTMP+1 ))
+ fi
+ if [[ ${NTMP} -gt 1 ]] ; then
+ g=$(echo "$(cd "$(dirname $tmp)" ; pwd)")
+ printf "${bold}${yellow}%-17s -- %s\n${normal}" "[WARNING]" "Found tmp folders from previous analyses in ${g}" | tee -a ${OUT}.wgrr.log
+ printf "${bold}${yellow}%-17s -- %s\n${normal}" "[WARNING]" "Consider deleting them" | tee -a ${OUT}.wgrr.log
+ fi
+done
+
if [[ $BATCHFLAG == 0 ]] ; then
if [[ $FAST == 1 ]] ; then
printf "${bold}${yellow}%-17s -- %s\n${normal}" "[WARNING]" "The fast flag (-f) is useless when not using sbatch" | tee -a ${OUT}.wgrr.log
@@ -291,6 +324,16 @@ STATS=($(awk '/^>/{p++;g=substr($1,2);gsub(/_[^_]+$/,"",g);if(!a[g]++){c++};LNR=
printf "%-17s -- %s %s %s %s %s\n" "["$(textifyDuration $SECONDS)"]" "Input file has" $STATS[1] "genomes and a total of" $STATS[2] "proteins" | tee -a ${OUT}.wgrr.log
printf "%-17s -- %s %s\n" "["$(textifyDuration $SECONDS)"]" "Mean number of proteins per genome:" $STATS[4] | tee -a ${OUT}.wgrr.log
+EST_M8_SIZE=$((STATS[1] * STATS[1] * STATS[4] / 10000000 ))
+
+if [[ ${EST_M8_SIZE} == 0 ]] ; then
+ printf "${bold}${yellow}%-17s -- %s\n${normal}" "[WARNING]" "Unable to estimate the MMseqs output file size." | tee -a ${OUT}.wgrr.log
+elif [[ ${EST_M8_SIZE} -gt 10 ]] ; then
+ if [[ ${NOM8} == 0 ]] ; then
+ printf "${bold}${yellow}%-17s -- %s\n${normal}" "[WARNING]" "MMseqs output file could exceed 10GB. Consider using the -n option to save disk space." | tee -a ${OUT}.wgrr.log
+ fi
+fi
+
if [[ $ARRAYSIZE == "AUTO" ]] ; then
if [[ ${STATS[4]} -le 100 ]] ; then
ARRAYSIZE=10000