From e18168a2a314b392b4d94bf89e6822946f9f47a4 Mon Sep 17 00:00:00 2001
From: jgugliel <julien.guglielmini@pasteur.fr>
Date: Thu, 24 Feb 2022 21:54:13 +0100
Subject: [PATCH] small fixes
---
wGRR | 5 ++++-
wGRR.awk | 2 +-
2 files changed, 5 insertions(+), 2 deletions(-)
diff --git a/wGRR b/wGRR
index 9bfb6e8..bfa5988 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 80492fa..4f91142 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" )
}
}
--
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