From c15abd2677f76717ba8043c46a87023a0a0179f4 Mon Sep 17 00:00:00 2001
From: Milton Silva <miltondts@gmail.com>
Date: Mon, 3 Aug 2020 11:03:10 +0100
Subject: [PATCH] Add scripts to run datasets

---
 benchmark/run_ref.sh     |  22 +-
 benchmark/run_reseq.sh   | 429 +++++++++++++++++++++++++++++++++++++++
 benchmark/run_vgeco2.sh  |  12 +-
 benchmark/run_virome.sh  | 280 +++++++++++++++++++++++++
 benchmark/run_vothers.sh | 344 ++++++++++++++++---------------
 5 files changed, 899 insertions(+), 188 deletions(-)
 create mode 100755 benchmark/run_reseq.sh
 create mode 100755 benchmark/run_virome.sh

diff --git a/benchmark/run_ref.sh b/benchmark/run_ref.sh
index 08a897d..bc43c8b 100755
--- a/benchmark/run_ref.sh
+++ b/benchmark/run_ref.sh
@@ -12,7 +12,7 @@ PARSE=0;
 RUN_GDC2=0;
 RUN_IDOCOMP=0;
 RUN_HRCM=0;
-RUN_GECO2=0;
+RUN_GECO2=1;
 RUN_GECO3=0;
 ###############################################################################
 #
@@ -34,22 +34,26 @@ if test -f "../../datasets/$1" && test -f "../../datasets/$2"; then
    cp ../../datasets/$1 .
    cp ../../datasets/$2 .
    rm -f xxx*
-   (time ./GDC2 c xxx $2 $1 ) &> ../../results/C_GDC_$1-$2
+   (/usr/bin/time -v ./GDC2 c xxx $2 $1 ) &> ../../results/C_GDC_$1-$2
    ls -la xxx.gdc2_rc | awk '{ print $5;}' > ../../results/BC_GDC_$1-$2
    rm -f $2 $1 xxx*;
 fi
 }
 #
 function RunGeCo2 {
-   PARAM=" -rm 20:500:1:35:0.95/3:100:0.95 -rm 13:200:1:1:0.95/0:0:0 -rm 10:10:0:0:0.95/0:0:0 ";
+    PARAMR=" -rm 20:500:1:35:0.95/3:100:0.95 -rm 13:200:1:1:0.95/0:0:0 -rm 10:10:0:0:0.95/0:0:0 -lr 0.03 -hs 64 ";
+    PARAMH=" -rm 20:500:1:35:0.95/3:100:0.95 -rm 13:200:1:1:0.95/0:0:0 -rm 10:10:0:0:0.95/0:0:0 -tm 4:1:0:1:0.9/0:0:0 -tm 17:100:1:10:0.95/2:20:0.95 -lr 0.03 -hs 64 ";
    # 1 - TARGET
    # 2 - REFERENCE
 if test -f "../../datasets/$1" && test -f "../../datasets/$2"; then
    cp ../../datasets/$1 .
    cp ../../datasets/$2 .
    rm -f $1.co
-   (time ./GeCo2 $PARAM -r $2 $1 ) &> ../../results/C_GECO2_REFO_$1-$2
-   ls -la $1.co | awk '{ print $5;}' > ../../results/BC_GECO2_REFO_$1-$2
+   (/usr/bin/time -v ./GeCo2 $PARAMR -r $2 $1 ) &> ../../results/C_GECO2R_REFO_$1-$2
+   ls -la $1.co | awk '{ print $5;}' > ../../results/BC_GECO2R_REFO_$1-$2
+
+   (/usr/bin/time -v ./GeCo2 $PARAMH -r $2 $1 ) &> ../../results/C_GECO2H_REFO_$1-$2
+   ls -la $1.co | awk '{ print $5;}' > ../../results/BC_GECO2H_REFO_$1-$2
    rm -f $2 $1 $1.co;
 fi
 }
@@ -63,10 +67,10 @@ if test -f "../../datasets/$1" && test -f "../../datasets/$2"; then
    cp ../../datasets/$1 .
    cp ../../datasets/$2 .
    rm -f $1.co
-   (time ./GeCo3 $PARAMR -r $2 $1 ) &> ../../results/C_GECO3R_REFO_$1-$2
+   (/usr/bin/time -v ./GeCo3 $PARAMR -r $2 $1 ) &> ../../results/C_GECO3R_REFO_$1-$2
    ls -la $1.co | awk '{ print $5;}' > ../../results/BC_GECO3R_REFO_$1-$2
 
-   (time ./GeCo3 $PARAMH -r $2 $1 ) &> ../../results/C_GECO3H_REFO_$1-$2
+   (/usr/bin/time -v ./GeCo3 $PARAMH -r $2 $1 ) &> ../../results/C_GECO3H_REFO_$1-$2
    ls -la $1.co | awk '{ print $5;}' > ../../results/BC_GECO3H_REFO_$1-$2
    rm -f $2 $1 $1.co;
 fi
@@ -79,7 +83,7 @@ if test -f "../../datasets-hrcm/$1.fasta" && test -f "../../datasets-hrcm/$2.fas
    cp ../../datasets-hrcm/$1.fasta .
    cp ../../datasets-hrcm/$2.fasta .
    rm -f $1.7z
-   (time ./hrcm compress -r $2.fasta -t $1.fasta ) &> ../../results/C_HRCM_REF_$1-$2
+   (/usr/bin/time -v ./hrcm compress -r $2.fasta -t $1.fasta ) &> ../../results/C_HRCM_REF_$1-$2
    ls -la $1.7z | awk '{ print $5;}' > ../../results/BC_HRCM_REF_$1-$2
    rm -f $2.fasta $1.fasta $1.7z;
 fi
@@ -98,7 +102,7 @@ if test -f "../../datasets/$1" && test -f "../../datasets/$2"; then
    (./generateSA.sh ref sa ) &> TIME_SA
    TIMEOFSA=`cat TIME_SA | grep "..." | awk '{ print $5;}'`
    echo "ref/$2.fa tar/$1.fa sa/$2.sa" > f.txt;
-   (./iDoComp.run c f.txt OUT ) &> ../../../results/C_IDOCOMP_$1-$2
+   (/usr/bin/time -v ./iDoComp.run c f.txt OUT ) &> ../../../results/C_IDOCOMP_$1-$2
    cat ../../../results/C_IDOCOMP_$1-$2 | grep "Compressed Size:" | awk '{ print $3; }' > ../../../results/BC_IDOCOMP_$1-$2
    CTIME=`cat ../../../results/C_IDOCOMP_$1-$2 | grep "CPU T" | awk '{print $4;}'`
    echo "$TIMEOFSA+$CTIME" | bc -l > ../../../results/CT_IDOCOMP_$1-$2
diff --git a/benchmark/run_reseq.sh b/benchmark/run_reseq.sh
new file mode 100755
index 0000000..abca615
--- /dev/null
+++ b/benchmark/run_reseq.sh
@@ -0,0 +1,429 @@
+#!/bin/bash
+###############################################################################
+INSTALL_GDC2=0;
+INSTALL_IDOCOMP=0;
+INSTALL_HRCM=0;
+INSTALL_GECO2=0;
+INSTALL_GECO3=0;
+###############################################################################
+DOWNLOAD=0;
+PARSE=1;
+###############################################################################
+RUN_GDC2=1;
+RUN_IDOCOMP=1;
+RUN_HRCM=1;
+RUN_GECO2=1;
+RUN_GECO3=1;
+###############################################################################
+#
+function Parse {
+if test -f "$1.fasta"; then
+    cat $1.fasta | grep -v ">" | tr -d -c "ACGT" > XTMP
+    cat HEADER XTMP > datasets/$1;
+    cp datasets/$1 datasets-hrcm/$1.fasta
+    fold -w80 datasets-hrcm/$1.fasta > XTMP
+    cp XTMP datasets-hrcm/$1.fasta
+    rm XTMP;
+fi
+}
+#
+function RunGDC2 {
+   # 1 - TARGET
+   # 2 - REFERENCE
+if test -f "../../datasets/$1" && test -f "../../datasets/$2"; then
+   cp ../../datasets/$1 .
+   cp ../../datasets/$2 .
+   rm -f xxx*
+   (/usr/bin/time -v ./GDC2 c xxx $2 $1 ) &> ../../results/C_GDC_$1-$2
+   ls -la xxx.gdc2_rc | awk '{ print $5;}' > ../../results/BC_GDC_$1-$2
+   rm -f $2 $1 xxx*;
+fi
+}
+#
+function RunGeCo2 {
+    PARAMR=" -rm 20:500:1:35:0.95/3:100:0.95 -rm 13:200:1:1:0.95/0:0:0 -rm 10:10:0:0:0.95/0:0:0 -lr 0.03 -hs 64 ";
+    PARAMH=" -rm 20:500:1:35:0.95/3:100:0.95 -rm 13:200:1:1:0.95/0:0:0 -rm 10:10:0:0:0.95/0:0:0 -tm 4:1:0:1:0.9/0:0:0 -tm 17:100:1:10:0.95/2:20:0.95 -lr 0.03 -hs 64 ";
+   # 1 - TARGET
+   # 2 - REFERENCE
+if test -f "../../datasets/$1" && test -f "../../datasets/$2"; then
+   cp ../../datasets/$1 .
+   cp ../../datasets/$2 .
+   rm -f $1.co
+   (/usr/bin/time -v ./GeCo2 $PARAMR -r $2 $1 ) &> ../../results/C_GECO2R_REFO_$1-$2
+   ls -la $1.co | awk '{ print $5;}' > ../../results/BC_GECO2R_REFO_$1-$2
+
+   (/usr/bin/time -v ./GeCo2 $PARAMH -r $2 $1 ) &> ../../results/C_GECO2H_REFO_$1-$2
+   ls -la $1.co | awk '{ print $5;}' > ../../results/BC_GECO2H_REFO_$1-$2
+   rm -f $2 $1 $1.co;
+fi
+}
+
+function RunGeCo3 {
+    PARAMR=" -rm 20:500:1:35:0.95/3:100:0.95 -rm 13:200:1:1:0.95/0:0:0 -rm 10:10:0:0:0.95/0:0:0 -lr 0.03 -hs 64 ";
+    PARAMH=" -rm 20:500:1:35:0.95/3:100:0.95 -rm 13:200:1:1:0.95/0:0:0 -rm 10:10:0:0:0.95/0:0:0 -tm 4:1:0:1:0.9/0:0:0 -tm 17:100:1:10:0.95/2:20:0.95 -lr 0.03 -hs 64 ";
+   # 1 - TARGET
+   # 2 - REFERENCE
+if test -f "../../datasets/$1" && test -f "../../datasets/$2"; then
+   cp ../../datasets/$1 .
+   cp ../../datasets/$2 .
+   rm -f $1.co
+   (/usr/bin/time -v ./GeCo3 $PARAMR -r $2 $1 ) &> ../../results/C_GECO3R_REFO_$1-$2
+   ls -la $1.co | awk '{ print $5;}' > ../../results/BC_GECO3R_REFO_$1-$2
+
+   (/usr/bin/time -v ./GeCo3 $PARAMH -r $2 $1 ) &> ../../results/C_GECO3H_REFO_$1-$2
+   ls -la $1.co | awk '{ print $5;}' > ../../results/BC_GECO3H_REFO_$1-$2
+   rm -f $2 $1 $1.co;
+fi
+}
+
+function RunHRCM {
+   # 1 - TARGET
+   # 2 - REFERENCE
+if test -f "../../datasets-hrcm/$1.fasta" && test -f "../../datasets-hrcm/$2.fasta"; then
+   cp ../../datasets-hrcm/$1.fasta .
+   cp ../../datasets-hrcm/$2.fasta .
+   rm -f $1.7z
+   (/usr/bin/time -v ./hrcm compress -r $2.fasta -t $1.fasta ) &> ../../results/C_HRCM_REF_$1-$2
+   ls -la $1.7z | awk '{ print $5;}' > ../../results/BC_HRCM_REF_$1-$2
+   rm -f $2.fasta $1.fasta $1.7z;
+fi
+}
+#
+function RunIDoComp {
+   # 1 - TARGET
+   # 2 - REFERENCE
+if test -f "../../datasets/$1" && test -f "../../datasets/$2"; then
+   cd sais-lite-2.4.1/
+   rm -fr sa ref tar
+   mkdir sa ref tar;
+   mkdir tmp_oneline_ref;
+   cp ../../../datasets/$1 tar/$1.fa
+   cp ../../../datasets/$2 ref/$2.fa
+   (./generateSA.sh ref sa ) &> TIME_SA
+   TIMEOFSA=`cat TIME_SA | grep "..." | awk '{ print $5;}'`
+   echo "ref/$2.fa tar/$1.fa sa/$2.sa" > f.txt;
+   (/usr/bin/time -v ./iDoComp.run c f.txt OUT ) &> ../../../results/C_IDOCOMP_$1-$2
+   cat ../../../results/C_IDOCOMP_$1-$2 | grep "Compressed Size:" | awk '{ print $3; }' > ../../../results/BC_IDOCOMP_$1-$2
+   CTIME=`cat ../../../results/C_IDOCOMP_$1-$2 | grep "CPU T" | awk '{print $4;}'`
+   echo "$TIMEOFSA+$CTIME" | bc -l > ../../../results/CT_IDOCOMP_$1-$2
+   rm -fr sa ref tar tmp_oneline_ref
+   cd ..
+fi
+}
+#
+###############################################################################
+# INSTALL
+mkdir -p datasets-hrcm
+mkdir -p datasets
+mkdir -p progs
+cd progs/
+###############################################################################
+# GET iDoComp
+#=================================================================
+if [[ "$INSTALL_IDOCOMP" -eq "1" ]]; then
+    rm -fr iDoComp/
+    git clone https://github.com/mikelhernaez/iDoComp.git
+    cd iDoComp/iDoComp_website_v1/sais-lite-2.4.1/source-code/
+    gcc -o ../sa.run sa_generator.c sais.c -lm
+    cd ../../simulations/source_code/
+    gcc -o ../../../sais-lite-2.4.1/iDoComp.run idc_generate_mapping.c main.c stats.c arith.c \
+	fasta_decompressor.c idc_load_chr.c os_stream.c fasta_compressor.c \
+	sam_stream.c -lm
+    cd ../../../../
+fi
+###############################################################################
+# GET GECO2
+#====================================================================
+if [[ "$INSTALL_GECO2" -eq "1" ]]; then
+   rm -fr geco2/
+   git clone https://github.com/cobilab/geco2.git
+   cd geco2/src/
+   cp Makefile.linux Makefile
+   sed -i 's/U32 garbage;//g' defs.h # fix for gcc 10
+   sed -i 's/garbage                   =//g' gede2.c # fix for gcc 10
+   make
+   cp GeCo2 ../
+   cp GeDe2 ../
+   cd ../../
+fi
+###############################################################################
+# GET GECO3
+#====================================================================
+if [[ "$INSTALL_GECO3" -eq "1" ]]; then
+   rm -fr geco3/
+   git clone https://github.com/cobilab/geco3.git
+   cd geco3/src/
+   make
+   cp GeCo3 ../
+   cp GeDe3 ../
+   cd ../../
+fi
+###############################################################################
+# GET GDC2
+#=====================================================================
+if [[ "$INSTALL_GDC2" -eq "1" ]]; then
+    rm -fr GDC2/
+    git clone https://github.com/refresh-bio/GDC2.git
+    cd GDC2/gdc_2/Gdc2/
+    # LIBRARIES ORDER ACCESS CREATE SOME PROBLES (WE ADD THEM TO THE END)
+    printf '\nall: gdc2 \n\nCC      = g++\nCFLAGS  = -Wall -O3 -m64 -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11\nCLINK   = -lm -O3 -m64 -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11 -lz \n\n.cpp.o: \n\t$(CC) $(CFLAGS) -c $< -o $@ \n\ngdc2: c1stage.o c2stage.o fasta.o hasher.o main.o p1stage.o qsmodel.o queue.o rangecod.o timer.o \n\t$(CC) $(CLINK) -o gdc2 c1stage.o c2stage.o fasta.o hasher.o main.o p1stage.o qsmodel.o queue.o rangecod.o timer.o ../libs/libaelf64.a -lz -lpthread \n\nclean: \n\trm gdc2 \n\trm *.o \n' > Makefile;
+    make clean ; make
+    cp gdc2 ../../GDC2 # TO NOT OVERLAP FOLDER NAME
+    cd ../../../
+fi
+###############################################################################
+# GET HRCM
+#====================================================================
+if [[ "$INSTALL_HRCM" -eq "1" ]]; then
+   rm -fr HRCM/
+   git clone https://github.com/haicy/HRCM.git
+   cd HRCM/
+   chmod +x 7za
+   make
+   cd ../
+fi
+##############################################################################
+cd ..
+###############################################################################
+# DOWNLOAD
+if [[ "$DOWNLOAD" -eq "1" ]]; then
+    echo "Downloading ..."
+fi
+# PARSE
+#=======================================================================
+if [[ "$PARSE" -eq "1" ]]; then
+   echo "Parsing ..."
+   echo ">X" > HEADER
+   #
+   Parse "HSK1_C1"
+   Parse "HSK1_C2"
+   Parse "HSK1_C3"
+   Parse "HSK1_C4"
+   Parse "HSK1_C5"
+   Parse "HSK1_C6"
+   Parse "HSK1_C7"
+   Parse "HSK1_C8"
+   Parse "HSK1_C9"
+   Parse "HSK1_C10"
+   Parse "HSK1_C11"
+   Parse "HSK1_C12"
+   Parse "HSK1_C13"
+   Parse "HSK1_C14"
+   Parse "HSK1_C15"
+   Parse "HSK1_C16"
+   Parse "HSK1_C17"
+   Parse "HSK1_C18"
+   Parse "HSK1_C19"
+   Parse "HSK1_C20"
+   Parse "HSK1_C21"
+   Parse "HSK1_C22"
+   Parse "HSK1_X"
+   Parse "HSK1_Y"
+   Parse "HSK1_M"
+   #
+   Parse "HSK2_C1"
+   Parse "HSK2_C2"
+   Parse "HSK2_C3"
+   Parse "HSK2_C4"
+   Parse "HSK2_C5"
+   Parse "HSK2_C6"
+   Parse "HSK2_C7"
+   Parse "HSK2_C8"
+   Parse "HSK2_C9"
+   Parse "HSK2_C10"
+   Parse "HSK2_C11"
+   Parse "HSK2_C12"
+   Parse "HSK2_C13"
+   Parse "HSK2_C14"
+   Parse "HSK2_C15"
+   Parse "HSK2_C16"
+   Parse "HSK2_C17"
+   Parse "HSK2_C18"
+   Parse "HSK2_C19"
+   Parse "HSK2_C20"
+   Parse "HSK2_C21"
+   Parse "HSK2_C22"
+   Parse "HSK2_X"
+   Parse "HSK2_Y"
+   Parse "HSK2_M"
+   #
+   echo "done!";
+   fi
+#
+# RUN
+#=========================================================================
+if [[ "$RUN_HRCM" -eq "1" ]]; then
+   echo "Running HRCM ...";
+   mkdir -p results
+   cd progs/HRCM
+   # target $1, reference $2:
+   RunHRCM "HSK1_C1" "HSK2_C1"
+   #RunHRCM "HSK1_C2" "HSK2_C2"
+   #RunHRCM "HSK1_C3" "HSK2_C3"
+   #RunHRCM "HSK1_C4" "HSK2_C4"
+   #RunHRCM "HSK1_C5" "HSK2_C5"
+   #RunHRCM "HSK1_C6" "HSK2_C6"
+   #RunHRCM "HSK1_C7" "HSK2_C7"
+   #RunHRCM "HSK1_C8" "HSK2_C8"
+   #RunHRCM "HSK1_C9" "HSK2_C9"
+   #RunHRCM "HSK1_C10" "HSK2_C10"
+   #RunHRCM "HSK1_C11" "HSK2_C11"
+   #RunHRCM "HSK1_C12" "HSK2_C12"
+   #RunHRCM "HSK1_C13" "HSK2_C13"
+   #RunHRCM "HSK1_C14" "HSK2_C14"
+   #RunHRCM "HSK1_C15" "HSK2_C15"
+   #RunHRCM "HSK1_C16" "HSK2_C16"
+   #RunHRCM "HSK1_C17" "HSK2_C17"
+   #RunHRCM "HSK1_C18" "HSK2_C18"
+   #RunHRCM "HSK1_C19" "HSK2_C19"
+   #RunHRCM "HSK1_C20" "HSK2_C20"
+   #RunHRCM "HSK1_C21" "HSK2_C21"
+   #RunHRCM "HSK1_C22" "HSK2_C22"
+   #RunHRCM "HSK1_X" "HSK2_X"
+   #RunHRCM "HSK1_Y" "HSK2_Y"
+   #RunHRCM "HSK1_M" "HSK2_M"
+   #
+   cd ../../
+   echo "Done!";
+fi
+
+if [[ "$RUN_GDC2" -eq "1" ]]; then
+   echo "Running GDC2 ...";
+   mkdir -p results
+   cd progs/GDC2
+   # target $1, reference $2:
+   RunGDC2 "HSK1_C1" "HSK2_C1"
+   #RunGDC2 "HSK1_C2" "HSK2_C2"
+   #RunGDC2 "HSK1_C3" "HSK2_C3"
+   #RunGDC2 "HSK1_C4" "HSK2_C4"
+   #RunGDC2 "HSK1_C5" "HSK2_C5"
+   #RunGDC2 "HSK1_C6" "HSK2_C6"
+   #RunGDC2 "HSK1_C7" "HSK2_C7"
+   #RunGDC2 "HSK1_C8" "HSK2_C8"
+   #RunGDC2 "HSK1_C9" "HSK2_C9"
+   #RunGDC2 "HSK1_C10" "HSK2_C10"
+   #RunGDC2 "HSK1_C11" "HSK2_C11"
+   #RunGDC2 "HSK1_C12" "HSK2_C12"
+   #RunGDC2 "HSK1_C13" "HSK2_C13"
+   #RunGDC2 "HSK1_C14" "HSK2_C14"
+   #RunGDC2 "HSK1_C15" "HSK2_C15"
+   #RunGDC2 "HSK1_C16" "HSK2_C16"
+   #RunGDC2 "HSK1_C17" "HSK2_C17"
+   #RunGDC2 "HSK1_C18" "HSK2_C18"
+   #RunGDC2 "HSK1_C19" "HSK2_C19"
+   #RunGDC2 "HSK1_C20" "HSK2_C20"
+   #RunGDC2 "HSK1_C21" "HSK2_C21"
+   #RunGDC2 "HSK1_C22" "HSK2_C22"
+   #RunGDC2 "HSK1_X" "HSK2_X"
+   #RunGDC2 "HSK1_Y" "HSK2_Y"
+   #RunGDC2 "HSK1_M" "HSK2_M"
+   #
+   cd ../../
+   echo "Done!";
+fi
+#==============================================================================
+if [[ "$RUN_IDOCOMP" -eq "1" ]]; then
+   echo "Running iDoComp ...";
+   mkdir -p results
+   cd progs/iDoComp
+   # target $1, reference $2:
+   RunIDoComp "HSK1_C1" "HSK2_C1"
+   #RunIDoComp "HSK1_C2" "HSK2_C2"
+   #RunIDoComp "HSK1_C3" "HSK2_C3"
+   #RunIDoComp "HSK1_C4" "HSK2_C4"
+   #RunIDoComp "HSK1_C5" "HSK2_C5"
+   #RunIDoComp "HSK1_C6" "HSK2_C6"
+   #RunIDoComp "HSK1_C7" "HSK2_C7"
+   #RunIDoComp "HSK1_C8" "HSK2_C8"
+   #RunIDoComp "HSK1_C9" "HSK2_C9"
+   #RunIDoComp "HSK1_C10" "HSK2_C10"
+   #RunIDoComp "HSK1_C11" "HSK2_C11"
+   #RunIDoComp "HSK1_C12" "HSK2_C12"
+   #RunIDoComp "HSK1_C13" "HSK2_C13"
+   #RunIDoComp "HSK1_C14" "HSK2_C14"
+   #RunIDoComp "HSK1_C15" "HSK2_C15"
+   #RunIDoComp "HSK1_C16" "HSK2_C16"
+   #RunIDoComp "HSK1_C17" "HSK2_C17"
+   #RunIDoComp "HSK1_C18" "HSK2_C18"
+   #RunIDoComp "HSK1_C19" "HSK2_C19"
+   #RunIDoComp "HSK1_C20" "HSK2_C20"
+   #RunIDoComp "HSK1_C21" "HSK2_C21"
+   #RunIDoComp "HSK1_C22" "HSK2_C22"
+   #RunIDoComp "HSK1_X" "HSK2_X"
+   #RunIDoComp "HSK1_Y" "HSK2_Y"
+   #RunIDoComp "HSK1_M" "HSK2_M"
+   #
+   cd ../../
+   echo "Done!";
+fi
+#==============================================================================
+if [[ "$RUN_GECO2" -eq "1" ]]; then
+   echo "Running GeCo2 ...";
+   mkdir -p results
+   cd progs/geco2
+   # target $1, reference $2:
+   RunGeCo2 "HSK1_C1" "HSK2_C1"
+   RunGeCo2 "HSK1_C2" "HSK2_C2"
+   RunGeCo2 "HSK1_C3" "HSK2_C3"
+   RunGeCo2 "HSK1_C4" "HSK2_C4"
+   RunGeCo2 "HSK1_C5" "HSK2_C5"
+   RunGeCo2 "HSK1_C6" "HSK2_C6"
+   RunGeCo2 "HSK1_C7" "HSK2_C7"
+   RunGeCo2 "HSK1_C8" "HSK2_C8"
+   RunGeCo2 "HSK1_C9" "HSK2_C9"
+   RunGeCo2 "HSK1_C10" "HSK2_C10"
+   RunGeCo2 "HSK1_C11" "HSK2_C11"
+   RunGeCo2 "HSK1_C12" "HSK2_C12"
+   RunGeCo2 "HSK1_C13" "HSK2_C13"
+   RunGeCo2 "HSK1_C14" "HSK2_C14"
+   RunGeCo2 "HSK1_C15" "HSK2_C15"
+   RunGeCo2 "HSK1_C16" "HSK2_C16"
+   RunGeCo2 "HSK1_C17" "HSK2_C17"
+   RunGeCo2 "HSK1_C18" "HSK2_C18"
+   RunGeCo2 "HSK1_C19" "HSK2_C19"
+   RunGeCo2 "HSK1_C20" "HSK2_C20"
+   RunGeCo2 "HSK1_C21" "HSK2_C21"
+   RunGeCo2 "HSK1_C22" "HSK2_C22"
+   RunGeCo2 "HSK1_X" "HSK2_X"
+   RunGeCo2 "HSK1_Y" "HSK2_Y"
+   RunGeCo2 "HSK1_M" "HSK2_M"
+   #
+   cd ../../
+   echo "Done!";
+fi
+
+if [[ "$RUN_GECO3" -eq "1" ]]; then
+   echo "Running GeCo3 ...";
+   mkdir -p results
+   cd progs/geco3
+   # target $1, reference $2:
+   RunGeCo3 "HSK1_C1" "HSK2_C1"
+   #RunGeCo3 "HSK1_C2" "HSK2_C2"
+   #RunGeCo3 "HSK1_C3" "HSK2_C3"
+   #RunGeCo3 "HSK1_C4" "HSK2_C4"
+   #RunGeCo3 "HSK1_C5" "HSK2_C5"
+   #RunGeCo3 "HSK1_C6" "HSK2_C6"
+   #RunGeCo3 "HSK1_C7" "HSK2_C7"
+   #RunGeCo3 "HSK1_C8" "HSK2_C8"
+   #RunGeCo3 "HSK1_C9" "HSK2_C9"
+   #RunGeCo3 "HSK1_C10" "HSK2_C10"
+   #RunGeCo3 "HSK1_C11" "HSK2_C11"
+   #RunGeCo3 "HSK1_C12" "HSK2_C12"
+   #RunGeCo3 "HSK1_C13" "HSK2_C13"
+   #RunGeCo3 "HSK1_C14" "HSK2_C14"
+   #RunGeCo3 "HSK1_C15" "HSK2_C15"
+   #RunGeCo3 "HSK1_C16" "HSK2_C16"
+   #RunGeCo3 "HSK1_C17" "HSK2_C17"
+   #RunGeCo3 "HSK1_C18" "HSK2_C18"
+   #RunGeCo3 "HSK1_C19" "HSK2_C19"
+   #RunGeCo3 "HSK1_C20" "HSK2_C20"
+   #RunGeCo3 "HSK1_C21" "HSK2_C21"
+   #RunGeCo3 "HSK1_C22" "HSK2_C22"
+   #RunGeCo3 "HSK1_X" "HSK2_X"
+   #RunGeCo3 "HSK1_Y" "HSK2_Y"
+   #RunGeCo3 "HSK1_M" "HSK2_M"
+   #
+   cd ../../
+   echo "Done!";
+fi
+###############################################################################
diff --git a/benchmark/run_vgeco2.sh b/benchmark/run_vgeco2.sh
index 9bbda55..280670d 100755
--- a/benchmark/run_vgeco2.sh
+++ b/benchmark/run_vgeco2.sh
@@ -15,9 +15,9 @@ function RunGeCo2 {
 if test -f "../../ds/$2"; then
    cp ../../ds/$2 .
    rm -f $2.co
-   (time ./GeCo2 $1 $2 ) &> ../../res/C_GECO2_$2
-   ls -la $2.co | awk '{ print $5;}' > ../../res/BC_GECO2_$2
-   rm -f $2 $2.co;
+   (/usr/bin/time -v ./GeCo2 $1 $2 ) &> ../../res/C_GECO2_LO_$2
+   ls -la $2.co | awk '{ print $5;}' > ../../res/BC_GECO2_LO_$2
+   #rm -f $2 $2.co;
 fi
 }
 
@@ -27,9 +27,9 @@ function RunGeCo3 {
 if test -f "../../ds/$2"; then
    cp ../../ds/$2 .
    rm -f $2.co
-   (time ./GeCo3 $1 $2 ) &> ../../res/C_GECO3_$2
-   ls -la $2.co | awk '{ print $5;}' > ../../res/BC_GECO3_$2
-   rm -f $2 $2.co;
+   (/usr/bin/time -v ./GeCo3 $1 $2 ) &> ../../res/C_GECO3_LO_$2
+   ls -la $2.co | awk '{ print $5;}' > ../../res/BC_GECO3_LO_$2
+   #rm -f $2 $2.co;
 fi
 }
 ###############################################################################
diff --git a/benchmark/run_virome.sh b/benchmark/run_virome.sh
new file mode 100755
index 0000000..59d5ce2
--- /dev/null
+++ b/benchmark/run_virome.sh
@@ -0,0 +1,280 @@
+#!/bin/bash
+###############################################################################
+INSTALL_NAF=0;
+INSTALL_GECO2=0;
+INSTALL_GECO3=0;
+###############################################################################
+DOWNLOAD=0;
+###############################################################################
+RUN_NAF=0;
+RUN_GECO2=1;
+RUN_GECO3=1;
+#
+function RunGeCo2 {
+   # 1 - params
+   # 2 - seq
+if test -f "../../ds/$2"; then
+   cp ../../ds/$2 .
+   rm -f $2.co
+   (/usr/bin/time -v ./GeCo2 -v $1 $2 ) &> ../../res/C_GECO2_l16_$2
+   ls -la $2.co | awk '{ print $5;}' > ../../res/BC_GECO2_l16_$2
+   rm -f $2 $2.co;
+fi
+}
+
+function RunGeCo3 {
+    # 1 - params
+    # 2 - seq
+if test -f "../../ds/$2"; then
+   cp ../../ds/$2 .
+   rm -f $2.co
+   (/usr/bin/time -v ./GeCo3 -v $1 $2 ) &> ../../res/C_GECO3_l16_$2
+   ls -la $2.co | awk '{ print $5;}' > ../../res/BC_GECO3_l16_$2
+   rm -f $2 $2.co;
+fi
+}
+
+function RunNAF {
+    # 1 - seq
+if test -f "../../ds/$1"; then
+   echo ">" > $1.fasta
+   cat ../../ds/$1 >> $1.fasta
+   rm -f $1.fasta.naf
+   (/usr/bin/time -v ./ENNAF --temp-dir /tmp -22 $1.fasta -o $1.naf ) &> ../../res/C_NAF_$1
+   ls -la $1.naf | awk '{ print $5;}' > ../../res/BC_NAF_$1
+   rm -f $1.fasta $1.naf;
+fi
+}
+
+function RunXM {
+    # 1 - seq
+if test -f "../../ds/$1"; then
+   echo ">" > $1.fasta
+   cat ../../ds/$1 >> $1.fasta
+
+   rm -f $1.xm
+   (/usr/bin/time -v ./XM --real=$1.xm $1.fasta ) &> ../../res/C_XM_$1
+   ls -la $1.xm | awk '{ print $5;}' > ../../res/BC_XM_$1
+   rm -f $1.fasta $1.xm;
+fi
+}
+
+function RunJARVIS {
+    # 1 - params
+    # 2 - seq
+if test -f "../../ds/$2"; then
+   cp ../../ds/$2 .
+   rm -f $2.jc
+   (/usr/bin/time -v ./JARVIS $1 $2 ) &> ../../res/C_JARVIS_$2
+   ls -la $2.jc | awk '{ print $5;}' > ../../res/BC_JARVIS_$2
+   rm -f $2 $2.jc;
+fi
+}
+
+function RunCMIX {
+    # 1 - seq
+if test -f "../../ds/$1"; then
+   cp ../../ds/$1 .
+   rm -f $1.cmix
+   (/usr/bin/time -v ./cmix -c $1 $1.cmix ) &> ../../res/C_CMIX_$1
+   ls -la $1.cmix | awk '{ print $5;}' > ../../res/BC_CMIX_$1
+   rm -f $1 $1.cmix;
+fi
+}
+
+function RunDEEPZIP {
+    # 1 - seq
+if test -f "../../ds/$1"; then
+   source tf/bin/activate
+   rm data/processed_files/*param.json data/processed_files/*npy
+   rm -rf data/files_to_be_compressed/
+   #rm -rf data/compressed/
+   mkdir -p data/files_to_be_compressed/
+   mkdir -p data/compressed/
+   cp ../../ds/$1 data/files_to_be_compressed/$1
+   cd data
+   ./run_parser.sh
+   cd ../src
+   (/usr/bin/time -v ./run_experiments.sh biGRU ) &> ../../../res/C_DEEPZIP_$1
+   cd ../data/compressed/
+   ls -la $1/biGRU.compressed.combined | awk '{ print $5;}' > ../../../../res/BC_DEEPZIP_$1
+   cd ../..
+fi
+}
+
+function RunZPAQ {
+    # 1 - seq
+if test -f "../../ds/$1"; then
+   cp ../../ds/$1 .
+   rm -f $1.zpaq
+   (/usr/bin/time -v ./zpaq a $1.zpaq $1  -m5 ) &> ../../res/C_ZPAQ_$1
+   ls -la $1.zpaq | awk '{ print $5;}' > ../../res/BC_ZPAQ_$1
+   rm -f $1 $1.zpaq;
+fi
+}
+
+#
+###############################################################################
+# INSTALL
+mkdir -p ds
+mkdir -p progs
+cd progs/
+###############################################################################
+# GET GECO2
+#====================================================================
+if [[ "$INSTALL_GECO2" -eq "1" ]]; then
+   rm -fr geco2/
+   git clone https://github.com/cobilab/geco2.git
+   cd geco2/src/
+   cp Makefile.linux Makefile
+   sed -i 's/U32 garbage;//g' defs.h # fix for gcc 10
+   sed -i 's/garbage                   =//g' gede2.c # fix for gcc 10
+   make
+   cp GeCo2 ../
+   cp GeDe2 ../
+   cd ../../
+fi
+###############################################################################
+# GET GECO3
+#====================================================================
+if [[ "$INSTALL_GECO3" -eq "1" ]]; then
+   rm -fr geco3/
+   git clone https://github.com/cobilab/geco3.git
+   cd geco3/src/
+   make
+   cp GeCo3 ../
+   cp GeDe3 ../
+   cd ../../
+fi
+###############################################################################
+# GET NAF
+#====================================================================
+if [[ "$INSTALL_NAF" -eq "1" ]]; then
+   rm -fr naf/
+   git clone --recurse-submodules https://github.com/KirillKryukov/naf.git
+   cd naf && make
+   cp ennaf/ennaf ENNAF # to avoid dir name collision
+   cd ../
+fi
+###############################################################################
+# GET XM
+#====================================================================
+if [[ "$INSTALL_XM" -eq "1" ]]; then
+    rm -fr japsa/
+    git clone https://github.com/mdcao/japsa.git
+    cd japsa
+    make install INSTALL_DIR=./xm MXMEM=7000m SERVER=true JLP=/usr/lib/jni
+    cp xm/bin/jsa.xm.compress XM
+    cd ../
+fi
+###############################################################################
+# GET JARVIS
+#====================================================================
+if [[ "$INSTALL_JARVIS" -eq "1" ]]; then
+    rm -fr jarvis/
+    git clone https://github.com/cobilab/jarvis.git
+    cd jarvis/src/
+    sed -i 's/uint32_t garbage;//g' defs.h # fix for gcc 10
+    make
+    cp JARVIS ../
+    cd ../../
+fi
+###############################################################################
+# GET CMIX
+#====================================================================
+if [[ "$INSTALL_CMIX" -eq "1" ]]; then
+    rm -fr cmix/
+    git clone https://github.com/byronknoll/cmix.git
+    cd cmix
+    make
+    cd ../
+fi
+###############################################################################
+# GET DEEPZIP
+#====================================================================
+if [[ "$INSTALL_DEEPZIP" -eq "1" ]]; then
+    rm -fr DeepZip/
+    git clone --single-branch --branch noGPU https://github.com/mohit1997/DeepZip.git
+    cd DeepZip
+    python3.6 -m venv tf
+    source tf/bin/activate
+    bash install.sh
+    deactivate
+    #params mentioned in paper
+    sed -i 's/batch_size=128/batch_size=1024/g' src/trainer.py
+    sed -i 's/num_epochs=20/num_epochs=3/g' src/trainer.py
+    #don't decompress
+    sed -i 's/\/usr\/bin\/time -v python decompressor.py/#\/usr\/bin\/time -v python decompressor.py/g' src/run_experiments.sh
+    sed -i 's/   cmp $recon_file_name/    #cmp $recon_file_name/g' src/run_experiments.sh
+    cd ../
+fi
+###############################################################################
+# GET ZPAQ
+#====================================================================
+if [[ "$INSTALL_ZPAQ" -eq "1" ]]; then
+    rm -fr zpaq/
+    git clone https://github.com/zpaq/zpaq.git
+    cd zpaq
+    g++ -O3 -march=native -Dunix zpaq.cpp libzpaq.cpp -pthread -o zpaq
+    cd ../
+fi
+
+##############################################################################
+cd ..
+###############################################################################
+# DOWNLOAD
+if [[ "$DOWNLOAD" -eq "1" ]]; then
+    echo "Downloading ..."
+    rm -rf ds/
+    mkdir ds/
+    cd ds
+
+    # ds4
+    wget https://tinyurl.com/DNAcorpus
+    unzip DNAcorpus
+    mv DNACorpus/* .
+    rm -f DNAcorpus 
+    rm -rf DNACorpus
+
+    cd ..
+fi
+#
+# RUN
+#=========================================================================
+###################################################################
+#### Specific
+if [[ "$RUN_NAF" -eq "1" ]]; then
+   echo "Running NAF ...";
+   mkdir -p res
+   cd progs/naf
+
+   RunNAF "virome"
+   #
+   cd ../../
+   echo "Done!";
+fi
+
+###############################################################################
+if [[ "$RUN_GECO2" -eq "1" ]]; then
+   echo "Running GeCo2 ...";
+   mkdir -p res
+   cd progs/geco2
+   PARAM_DS1="-tm 7:1:1:1:0.8/0:0:0 -tm 13:10:0:1:0.95/0:0:0 -tm 19:500:1:40:0.95/5:20:0.95 -ls 0.03 -hs 64"
+   RunGeCo2 "$PARAM_DS1" "virome"
+   #
+   cd ../../
+   echo "Done!";
+fi
+
+if [[ "$RUN_GECO3" -eq "1" ]]; then
+   echo "Running GeCo3 ...";
+   mkdir -p res
+   cd progs/geco3
+
+   PARAM_DS1="-tm 7:1:1:1:0.8/0:0:0 -tm 13:10:0:1:0.95/0:0:0 -tm 19:500:1:40:0.95/5:20:0.95 -ls 0.03 -hs 64"
+   RunGeCo3 "$PARAM_DS1" "virome"
+   
+   #
+   cd ../../
+   echo "Done!";
+fi
diff --git a/benchmark/run_vothers.sh b/benchmark/run_vothers.sh
index d39ad5a..8105b12 100755
--- a/benchmark/run_vothers.sh
+++ b/benchmark/run_vothers.sh
@@ -14,7 +14,7 @@ DOWNLOAD=0;
 RUN_NAF=0;
 RUN_XM=0;
 RUN_JARVIS=0;
-RUN_CMIX=0;
+RUN_CMIX=1;
 RUN_DEEPZIP=0;
 RUN_ZPAQ=0;
 RUN_GECO2=0;
@@ -26,7 +26,7 @@ function RunGeCo2 {
 if test -f "../../ds/$2"; then
    cp ../../ds/$2 .
    rm -f $2.co
-   (time ./GeCo2 $1 $2 ) &> ../../res/C_GECO2_l16_$2
+   (/usr/bin/time -v ./GeCo2 -v $1 $2 ) &> ../../res/C_GECO2_l16_$2
    ls -la $2.co | awk '{ print $5;}' > ../../res/BC_GECO2_l16_$2
    rm -f $2 $2.co;
 fi
@@ -38,7 +38,7 @@ function RunGeCo3 {
 if test -f "../../ds/$2"; then
    cp ../../ds/$2 .
    rm -f $2.co
-   (time ./GeCo3 $1 $2 ) &> ../../res/C_GECO3_l16_$2
+   (/usr/bin/time -v ./GeCo3 -v $1 $2 ) &> ../../res/C_GECO3_l16_$2
    ls -la $2.co | awk '{ print $5;}' > ../../res/BC_GECO3_l16_$2
    rm -f $2 $2.co;
 fi
@@ -50,7 +50,7 @@ if test -f "../../ds/$1"; then
    echo ">" > $1.fasta
    cat ../../ds/$1 >> $1.fasta
    rm -f $1.fasta.naf
-   (time ./ENNAF --temp-dir /tmp -22 $1.fasta -o $1.naf ) &> ../../res/C_NAF_$1
+   (/usr/bin/time -v ./ENNAF --temp-dir /tmp -22 $1.fasta -o $1.naf ) &> ../../res/C_NAF_$1
    ls -la $1.naf | awk '{ print $5;}' > ../../res/BC_NAF_$1
    rm -f $1.fasta $1.naf;
 fi
@@ -63,7 +63,7 @@ if test -f "../../ds/$1"; then
    cat ../../ds/$1 >> $1.fasta
 
    rm -f $1.xm
-   (time ./XM --real=$1.xm $1.fasta ) &> ../../res/C_XM_$1
+   (/usr/bin/time -v ./XM --real=$1.xm $1.fasta ) &> ../../res/C_XM_$1
    ls -la $1.xm | awk '{ print $5;}' > ../../res/BC_XM_$1
    rm -f $1.fasta $1.xm;
 fi
@@ -75,7 +75,7 @@ function RunJARVIS {
 if test -f "../../ds/$2"; then
    cp ../../ds/$2 .
    rm -f $2.jc
-   (time ./JARVIS $1 $2 ) &> ../../res/C_JARVIS_$2
+   (/usr/bin/time -v ./JARVIS $1 $2 ) &> ../../res/C_JARVIS_$2
    ls -la $2.jc | awk '{ print $5;}' > ../../res/BC_JARVIS_$2
    rm -f $2 $2.jc;
 fi
@@ -86,7 +86,7 @@ function RunCMIX {
 if test -f "../../ds/$1"; then
    cp ../../ds/$1 .
    rm -f $1.cmix
-   (time ./cmix -c $1 $1.cmix ) &> ../../res/C_CMIX_$1
+   (/usr/bin/time -v ./cmix -c $1 $1.cmix ) &> ../../res/C_CMIX_$1
    ls -la $1.cmix | awk '{ print $5;}' > ../../res/BC_CMIX_$1
    rm -f $1 $1.cmix;
 fi
@@ -105,11 +105,10 @@ if test -f "../../ds/$1"; then
    cd data
    ./run_parser.sh
    cd ../src
-   (time ./run_experiments.sh biGRU ) &> ../../../res/C_DEEPZIP_$1
+   (/usr/bin/time -v ./run_experiments.sh biGRU ) &> ../../../res/C_DEEPZIP_$1
    cd ../data/compressed/
    ls -la $1/biGRU.compressed.combined | awk '{ print $5;}' > ../../../../res/BC_DEEPZIP_$1
    cd ../..
-   #rm -rf data/files_to_be_compressed/$1 data/compressed/$1;
 fi
 }
 
@@ -118,7 +117,7 @@ function RunZPAQ {
 if test -f "../../ds/$1"; then
    cp ../../ds/$1 .
    rm -f $1.zpaq
-   (time ./zpaq a $1.zpaq $1  -m5 ) &> ../../res/C_ZPAQ_$1
+   (/usr/bin/time -v ./zpaq a $1.zpaq $1  -m5 ) &> ../../res/C_ZPAQ_$1
    ls -la $1.zpaq | awk '{ print $5;}' > ../../res/BC_ZPAQ_$1
    rm -f $1 $1.zpaq;
 fi
@@ -247,102 +246,132 @@ if [[ "$DOWNLOAD" -eq "1" ]]; then
     rm -f DNAcorpus 
     rm -rf DNACorpus
 
-    #ds1
-    wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/067/695/GCA_900067695.1_Pabies01/GCA_900067695.1_Pabies01_genomic.fna.gz
-    
     cd ..
 fi
 #
 # RUN
 #=========================================================================
-if [[ "$RUN_GECO2" -eq "1" ]]; then
-    echo "Running GeCo2 ...";
-    # l 16 equiv
-    PARAM_DS4="-tm 1:1:0:0:0.9/0:0:0 -tm 2:1:0:0:0.78/0:0:0 -tm 3:1:0:0:0.9/0:0:0 -tm 4:1:1:0:0.78/0:0:0 -tm 5:10:1:1:0.90/0:0:0 -tm 6:1:1:0:0.85/0:0:0 -tm 7:1:1:0:0.85/0:0:0 -tm 8:1:1:0:0.91/0:0:0 -tm 9:10:0:0:0.9/0:0:0 -tm 10:10:0:0:0.9/0:0:0 -tm 11:10:0:0:0.9/0:0:0 -tm 12:20:1:1:0.94/0:0:0 -tm 13:10:1:0:0.95/0:0:0 -tm 14:50:1:1:0.95/0:0:0 -tm 16:200:1:10:0.95/1:50:0.95 -tm 17:100:1:20:0.9/3:10:0.9 -tm 20:500:1:30:0.95/2:20:0.95"
-    
+## Gen purpose
+if [[ "$RUN_CMIX" -eq "1" ]]; then
+   echo "Running CMIX ...";
    mkdir -p res
-   cd progs/geco2
+   cd progs/cmix
 
    #ds4
-   RunGeCo2 "-l 1 -lr 0.06 -hs 8" "BuEb"
-   RunGeCo2 "-l 2 -lr 0.06 -hs 16" "AgPh"
-   RunGeCo2 "-l 3 -lr 0.09 -hs 24" "YeMi"
-   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "HePy"
-   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "AeCa"
-   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "HaHi"
-   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "EsCo"
-   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "PlFa"
-   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "ScPo"
-   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "EnIn"
-   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "DrMe"
-   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "OrSa"
-   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "DaRe"
-   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "GaGa"
-   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "HoSa"
+   #RunCMIX  "BuEb"
+   #RunCMIX  "AgPh"
+   #RunCMIX  "YeMi"
+   #RunCMIX  "HePy"
+   #RunCMIX  "AeCa"
+   #RunCMIX  "HaHi"
+   #RunCMIX  "EsCo"
+   #RunCMIX  "PlFa"
+   #RunCMIX  "ScPo"
+   #RunCMIX  "EnIn"
+   RunCMIX  "HoSaY"
+   RunCMIX  "DrMe"
+   RunCMIX  "OrSa"
+   RunCMIX  "DaRe"
+   RunCMIX  "GaGa"
+   RunCMIX  "HoSa"
 
    #ds2 and ds3
-   PARAM_DS23="-tm 3:1:1:1:0.8/0:0:0 -tm 6:1:1:1:0.85/0:0:0 -tm 9:1:1:1:0.85/0:0:0 -tm 12:10:0:1:0.85/0:0:0 -tm 15:200:1:10:0.85/2:1:0.85 -tm 17:200:1:10:0.85/2:1:0.85 -tm 20:500:1:40:0.85/5:20:0.85 -lr 0.03 -hs 64"
+   #RunCMIX  "HoSaY"
+   #RunCMIX  "Mitochondrion"
+
+   #RunCMIX  "VDB"
+   #RunCMIX  "Archaea"
+
+   #ds1
+   #RunCMIX "GoGoC"
+   #RunCMIX "PaTrC"
+   #RunCMIX "HoSaC"
+   #RunCMIX "PiAbC"
+   #
+   cd ../../
+   echo "Done!";
+fi
+
+if [[ "$RUN_DEEPZIP" -eq "1" ]]; then
+   echo "Running DEEPZIP ...";
+   mkdir -p res
+   cd progs/DeepZip
 
-   RunGeCo2 PARAM_DS23 "HoSaY"
-   RunGeCo2 PARAM_DS23 "Mitochondrion"
+   #ds4 System reboots with larger files (>= AeCa)
+   #RunDEEPZIP  "BuEb"
+   #RunDEEPZIP  "AgPh"
+   #RunDEEPZIP  "YeMi"
+   #RunDEEPZIP  "HePy"
+   #RunDEEPZIP  "AeCa"
+   RunDEEPZIP  "HaHi"
+   RunDEEPZIP  "EsCo"
+   RunDEEPZIP  "PlFa"
+   RunDEEPZIP  "ScPo"
+   RunDEEPZIP  "EnIn"
+   #RunDEEPZIP  "DrMe"
+   #RunDEEPZIP  "OrSa"
+   #RunDEEPZIP  "DaRe"
+   #RunDEEPZIP  "GaGa"
+   #RunDEEPZIP  "HoSa"
 
-   RunGeCo2 PARAM_DS23 "VDB"
-   RunGeCo2 PARAM_DS23 "Archaea"
+   #ds2 and ds3
+   #RunDEEPZIP  "HoSaY"
+   #RunDEEPZIP  "Mitochondrion"
+
+   #RunDEEPZIP  "VDB"
+   #RunDEEPZIP  "Archaea"
 
    #ds1
-   PARAM_DS1="-tm 3:1:1:1:0.70/0:0:0 -tm 8:1:1:1:0.85/0:0:0 -tm 13:10:0:1:0.85/0:0:0 -tm 19:500:1:40:0.85/5:20:0.85 -ls 0.03 -hs 64"
-   RunGeCo2 PARAM_DS1 "GoGoC"
-   RunGeCo2 PARAM_DS1 "PaTrC"
-   RunGeCo2 PARAM_DS1 "HoSaC"
-   RunGeCo2 PARAM_DS1 "PiAbC"
+   #RunDEEPZIP "GoGoC"
+   #RunDEEPZIP "PaTrC"
+   #RunDEEPZIP "HoSaC"
+   #RunDEEPZIP "PiAbC"
    #
    cd ../../
    echo "Done!";
 fi
 
-if [[ "$RUN_GECO3" -eq "1" ]]; then
-   echo "Running GeCo3 ...";
+
+if [[ "$RUN_ZPAQ" -eq "1" ]]; then
+   echo "Running ZPAQ ...";
    mkdir -p res
-   cd progs/geco3
+   cd progs/zpaq
 
    #ds4
-   RunGeCo3 "-l 1 -lr 0.06 -hs 8" "BuEb"
-   RunGeCo3 "-l 2 -lr 0.06 -hs 16" "AgPh"
-   RunGeCo3 "-l 3 -lr 0.09 -hs 24" "YeMi"
-   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "HePy"
-   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "AeCa"
-   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "HaHi"
-   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "EsCo"
-   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "PlFa"
-   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "ScPo"
-   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "EnIn"
-   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "DrMe"
-   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "OrSa"
-   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "DaRe"
-   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "GaGa"
-   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "HoSa"
+   RunZPAQ  "BuEb"
+   RunZPAQ  "AgPh"
+   RunZPAQ  "YeMi"
+   RunZPAQ  "HePy"
+   RunZPAQ  "AeCa"
+   RunZPAQ  "HaHi"
+   RunZPAQ  "EsCo"
+   RunZPAQ  "PlFa"
+   RunZPAQ  "ScPo"
+   RunZPAQ  "EnIn"
+   RunZPAQ  "DrMe"
+   RunZPAQ  "OrSa"
+   RunZPAQ  "DaRe"
+   RunZPAQ  "GaGa"
+   RunZPAQ  "HoSa"
 
    #ds2 and ds3
-   PARAM_DS23="-tm 3:1:1:1:0.8/0:0:0 -tm 6:1:1:1:0.85/0:0:0 -tm 9:1:1:1:0.85/0:0:0 -tm 12:10:0:1:0.85/0:0:0 -tm 15:200:1:10:0.85/2:1:0.85 -tm 17:200:1:10:0.85/2:1:0.85 -tm 20:500:1:40:0.85/5:20:0.85 -lr 0.03 -hs 64"
-
-   RunGeCo3 PARAM_DS23 "HoSaY"
-   RunGeCo3 PARAM_DS23 "Mitochondrion"
+   RunZPAQ  "HoSaY"
+   RunZPAQ  "Mitochondrion"
 
-   RunGeCo3 PARAM_DS23 "VDB"
-   RunGeCo3 PARAM_DS23 "Archaea"
+   RunZPAQ  "VDB"
+   RunZPAQ  "Archaea"
 
    #ds1
-   PARAM_DS1="-tm 3:1:1:1:0.70/0:0:0 -tm 8:1:1:1:0.85/0:0:0 -tm 13:10:0:1:0.85/0:0:0 -tm 19:500:1:40:0.85/5:20:0.85 -ls 0.03 -hs 64"
-   RunGeCo3 PARAM_DS1 "GoGoC"
-   RunGeCo3 PARAM_DS1 "PaTrC"
-   RunGeCo3 PARAM_DS1 "HoSaC"
-   RunGeCo3 PARAM_DS1 "PiAbC"
-   
+   RunZPAQ "GoGoC"
+   RunZPAQ "PaTrC"
+   RunZPAQ "HoSaC"
+   RunZPAQ "PiAbC"
    #
    cd ../../
    echo "Done!";
 fi
-
+###################################################################
+#### Specific
 if [[ "$RUN_NAF" -eq "1" ]]; then
    echo "Running NAF ...";
    mkdir -p res
@@ -411,11 +440,11 @@ if [[ "$RUN_XM" -eq "1" ]]; then
    RunXM  "VDB"
    RunXM  "Archaea"
 
-   #ds1
-   RunXM "GoGoC"
-   RunXM "PaTrC"
-   RunXM "HoSaC"
-   RunXM "PiAbC"
+   #ds1 ERROR can't compress
+   #RunXM "GoGoC"
+   #RunXM "PaTrC"
+   #RunXM "HoSaC"
+   #RunXM "PiAbC"
    #
    cd ../../
    echo "Done!";
@@ -450,7 +479,7 @@ if [[ "$RUN_JARVIS" -eq "1" ]]; then
    RunJARVIS "-l 7"  "VDB"
    RunJARVIS "-l 7"  "Archaea"
 
-   #ds1
+   #ds1 OOM with 32GB
    #RunJARVIS "-l 7" "GoGoC"
    #RunJARVIS "-l 7" "PaTrC"
    #RunJARVIS "-l 7" "HoSaC"
@@ -460,120 +489,89 @@ if [[ "$RUN_JARVIS" -eq "1" ]]; then
    echo "Done!";
 fi
 ###############################################################################
-## Gen purpose
-if [[ "$RUN_CMIX" -eq "1" ]]; then
-   echo "Running CMIX ...";
+if [[ "$RUN_GECO2" -eq "1" ]]; then
+    echo "Running GeCo2 ...";
+    # l 16 equiv
+    PARAM_DS4="-tm 1:1:0:0:0.9/0:0:0 -tm 2:1:0:0:0.78/0:0:0 -tm 3:1:0:0:0.9/0:0:0 -tm 4:1:1:0:0.78/0:0:0 -tm 5:10:1:1:0.90/0:0:0 -tm 6:1:1:0:0.85/0:0:0 -tm 7:1:1:0:0.85/0:0:0 -tm 8:1:1:0:0.91/0:0:0 -tm 9:10:0:0:0.9/0:0:0 -tm 10:10:0:0:0.9/0:0:0 -tm 11:10:0:0:0.9/0:0:0 -tm 12:20:1:1:0.94/0:0:0 -tm 13:10:1:0:0.95/0:0:0 -tm 14:50:1:1:0.95/0:0:0 -tm 16:200:1:10:0.95/1:50:0.95 -tm 17:100:1:20:0.9/3:10:0.9 -tm 20:500:1:30:0.95/2:20:0.95"
+    
    mkdir -p res
-   cd progs/cmix
+   cd progs/geco2
 
    #ds4
-   RunCMIX  "BuEb"
-   RunCMIX  "AgPh"
-   RunCMIX  "YeMi"
-   RunCMIX  "HePy"
-   RunCMIX  "AeCa"
-   RunCMIX  "HaHi"
-   RunCMIX  "EsCo"
-   RunCMIX  "PlFa"
-   #RunCMIX  "ScPo"
-   #RunCMIX  "EnIn"
-   #RunCMIX  "DrMe"
-   #RunCMIX  "OrSa"
-   #RunCMIX  "DaRe"
-   #RunCMIX  "GaGa"
-   #RunCMIX  "HoSa"
+   RunGeCo2 "-l 1 -lr 0.06 -hs 8" "BuEb"
+   RunGeCo2 "-l 2 -lr 0.06 -hs 16" "AgPh"
+   RunGeCo2 "-l 3 -lr 0.09 -hs 24" "YeMi"
+   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "HePy"
+   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "AeCa"
+   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "HaHi"
+   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "EsCo"
+   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "PlFa"
+   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "ScPo"
+   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "EnIn"
+   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "DrMe"
+   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "OrSa"
+   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "DaRe"
+   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "GaGa"
+   RunGeCo2 "$PARAM_DS4 -lr 0.03 -hs 64" "HoSa"
 
    #ds2 and ds3
-   #RunCMIX  "HoSaY"
-   #RunCMIX  "Mitochondrion"
-
-   #RunCMIX  "VDB"
-   #RunCMIX  "Archaea"
-
-   #ds1
-   #RunCMIX "GoGoC"
-   #RunCMIX "PaTrC"
-   #RunCMIX "HoSaC"
-   #RunCMIX "PiAbC"
-   #
-   cd ../../
-   echo "Done!";
-fi
-
-if [[ "$RUN_DEEPZIP" -eq "1" ]]; then
-   echo "Running DEEPZIP ...";
-   mkdir -p res
-   cd progs/DeepZip
-
-   #ds4
-   RunDEEPZIP  "BuEb"
-   RunDEEPZIP  "AgPh"
-   RunDEEPZIP  "YeMi"
-   RunDEEPZIP  "HePy"
-   RunDEEPZIP  "AeCa"
-   RunDEEPZIP  "HaHi"
-   RunDEEPZIP  "EsCo"
-   RunDEEPZIP  "PlFa"
-   #RunDEEPZIP  "ScPo"
-   #RunDEEPZIP  "EnIn"
-   #RunDEEPZIP  "DrMe"
-   #RunDEEPZIP  "OrSa"
-   #RunDEEPZIP  "DaRe"
-   #RunDEEPZIP  "GaGa"
-   #RunDEEPZIP  "HoSa"
+   PARAM_DS23="-tm 3:1:1:1:0.8/0:0:0 -tm 6:1:1:1:0.85/0:0:0 -tm 9:1:1:1:0.85/0:0:0 -tm 12:10:0:1:0.85/0:0:0 -tm 15:200:1:10:0.85/2:1:0.85 -tm 17:200:1:10:0.85/2:1:0.85 -tm 20:500:1:40:0.85/5:20:0.85 -lr 0.03 -hs 64"
 
-   #ds2 and ds3
-   #RunDEEPZIP  "HoSaY"
-   #RunDEEPZIP  "Mitochondrion"
+   RunGeCo2 "$PARAM_DS23" "HoSaY"
+   RunGeCo2 "$PARAM_DS23" "Mitochondrion"
 
-   #RunDEEPZIP  "VDB"
-   #RunDEEPZIP  "Archaea"
+   RunGeCo2 "$PARAM_DS23" "VDB"
+   RunGeCo2 "$PARAM_DS23" "Archaea"
 
    #ds1
-   #RunDEEPZIP "GoGoC"
-   #RunDEEPZIP "PaTrC"
-   #RunDEEPZIP "HoSaC"
-   #RunDEEPZIP "PiAbC"
+   PARAM_DS1="-tm 3:1:1:1:0.70/0:0:0 -tm 8:1:1:1:0.85/0:0:0 -tm 13:10:0:1:0.85/0:0:0 -tm 19:500:1:40:0.85/5:20:0.85 -ls 0.03 -hs 64"
+   RunGeCo2 "$PARAM_DS1" "GoGoC"
+   RunGeCo2 "$PARAM_DS1" "PaTrC"
+   RunGeCo2 "$PARAM_DS1" "HoSaC"
+   RunGeCo2 "$PARAM_DS1" "PiAbC"
    #
    cd ../../
    echo "Done!";
 fi
 
-
-if [[ "$RUN_ZPAQ" -eq "1" ]]; then
-   echo "Running ZPAQ ...";
+if [[ "$RUN_GECO3" -eq "1" ]]; then
+   echo "Running GeCo3 ...";
    mkdir -p res
-   cd progs/zpaq
+   cd progs/geco3
 
    #ds4
-   RunZPAQ  "BuEb"
-   RunZPAQ  "AgPh"
-   RunZPAQ  "YeMi"
-   RunZPAQ  "HePy"
-   RunZPAQ  "AeCa"
-   RunZPAQ  "HaHi"
-   RunZPAQ  "EsCo"
-   RunZPAQ  "PlFa"
-   RunZPAQ  "ScPo"
-   RunZPAQ  "EnIn"
-   RunZPAQ  "DrMe"
-   RunZPAQ  "OrSa"
-   RunZPAQ  "DaRe"
-   RunZPAQ  "GaGa"
-   RunZPAQ  "HoSa"
+   RunGeCo3 "-l 1 -lr 0.06 -hs 8" "BuEb"
+   RunGeCo3 "-l 2 -lr 0.06 -hs 16" "AgPh"
+   RunGeCo3 "-l 3 -lr 0.09 -hs 24" "YeMi"
+   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "HePy"
+   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "AeCa"
+   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "HaHi"
+   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "EsCo"
+   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "PlFa"
+   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "ScPo"
+   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "EnIn"
+   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "DrMe"
+   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "OrSa"
+   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "DaRe"
+   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "GaGa"
+   RunGeCo3 "-l 16 -lr 0.03 -hs 64" "HoSa"
 
    #ds2 and ds3
-   RunZPAQ  "HoSaY"
-   RunZPAQ  "Mitochondrion"
+   PARAM_DS23="-tm 3:1:1:1:0.8/0:0:0 -tm 6:1:1:1:0.85/0:0:0 -tm 9:1:1:1:0.85/0:0:0 -tm 12:10:0:1:0.85/0:0:0 -tm 15:200:1:10:0.85/2:1:0.85 -tm 17:200:1:10:0.85/2:1:0.85 -tm 20:500:1:40:0.85/5:20:0.85 -lr 0.03 -hs 64"
 
-   RunZPAQ  "VDB"
-   RunZPAQ  "Archaea"
+   RunGeCo3 "$PARAM_DS23" "HoSaY"
+   RunGeCo3 "$PARAM_DS23" "Mitochondrion"
+
+   RunGeCo3 "$PARAM_DS23" "VDB"
+   RunGeCo3 "$PARAM_DS23" "Archaea"
 
    #ds1
-   RunZPAQ "GoGoC"
-   RunZPAQ "PaTrC"
-   RunZPAQ "HoSaC"
-   RunZPAQ "PiAbC"
+   PARAM_DS1="-tm 3:1:1:1:0.70/0:0:0 -tm 8:1:1:1:0.85/0:0:0 -tm 13:10:0:1:0.85/0:0:0 -tm 19:500:1:40:0.85/5:20:0.85 -ls 0.03 -hs 64"
+   RunGeCo3 "$PARAM_DS1" "GoGoC"
+   RunGeCo3 "$PARAM_DS1" "PaTrC"
+   RunGeCo3 "$PARAM_DS1" "HoSaC"
+   RunGeCo3 "$PARAM_DS1" "PiAbC"
+   
    #
    cd ../../
    echo "Done!";