diff --git a/wGRR b/wGRR index 9bfb6e8e5bdf1c81f7347bc1f93fbcf16fa2fdee..bfa59884c71d0bfb790b8fe203731ca766c8c19d 100755 --- a/wGRR +++ b/wGRR @@ -12,6 +12,8 @@ readonly VERSION=0.5 bold=$(tput bold) normal=$(tput sgr0) +ALL_ARGS=($@) + display_usage() { echo "wGRR version ${VERSION}" echo "${bold}USAGE:${normal} $ZSH_ARGZERO -f <fasta_file> [OPTIONS]" @@ -156,7 +158,7 @@ echo "[INFO] -- wGRR version ${VERSION}" if [[ $BATCHFLAG == 0 ]] ; then echo "[INFO] -- The command is:" - echo "[INFO] -- ./wGRR "$@ + echo "[INFO] -- ./wGRR ${ALL_ARGS}" if [[ $THREADS -gt $(nproc) ]] ; then echo "[ERROR] -- You required $THREADS threads but your machine has $(nproc) cores." @@ -301,6 +303,7 @@ else REQMEM="" echo "[INFO] -- Estimating required memory" M1=$(awk -f wGRR.awk -v MINP=1 -v MAXP=10 -v OUT=$OUT -v MEM=1 $OUT.allpairs.txt $PRT $OUT.m8) + echo $M1 REQMEM=$(bc -l <<< $(numfmt --from=iec $M1)*($ARRAYSIZE/10) | numfmt --to=iec | awk '{U=$0;gsub(/[^A-Za-z]/,"",U);V=$0;gsub(/[A-Za-z]+$/,"",V);split(V,a,".");n=split(a[1],b,"");c=b[1]+1;i=1;while(++i<=n){c=c"0"}print c""U}') echo "[INFO] -- $REQMEM per job required" duration=$SECONDS diff --git a/wGRR.awk b/wGRR.awk index 80492fa506f7ad8e29e6e8af204b77e576dce14a..4f911429f269c442f8bdfeca90f71305be661ab2 100755 --- a/wGRR.awk +++ b/wGRR.awk @@ -296,6 +296,6 @@ END { } } if(MEM){ - system("ps -www -o rss=,command= | grep wGRR.awk | grep "OUT" | sort -rn | awk '{print $1;exit}' | numfmt --to=iec" ) + system("ps -wo rss,comm | grep wGRR.awk | grep "OUT" | sort -rn | awk '{print $1;exit}' | numfmt --from-unit=1024 --to=iec" ) } }