Commit 2e0c5b84 authored by Shaman Narayanasamy's avatar Shaman Narayanasamy
Browse files

Add new launcher and modify execution and launcher scripts

parent c345607e
...@@ -13,16 +13,18 @@ MOCAT_MG=$7 ...@@ -13,16 +13,18 @@ MOCAT_MG=$7
IMP_MT=$8 IMP_MT=$8
METAMOS_MT=$9 METAMOS_MT=$9
MOCAT_MT=${10} MOCAT_MT=${10}
NAIVE=${11}
OUTDIR=${11} OUTDIR=${12}
date date
#source ../preload_modules.sh #source ../preload_modules.sh
/mnt/gaiagpfs/projects/ecosystem_biology/local_tools/quast/metaquast.py \ /mnt/gaiagpfs/projects/ecosystem_biology/local_tools/quast/metaquast.py \
-o $OUTDIR -t 12 \ -o $OUTDIR -t 6 \
-l "IMP, IMP-megahit, MetAmos_MGMT, MOCAT_MGMT, IMP_MG, MetAmos_MG, MOCAT_MG, IMP_MT, MetAmos_MT, MOCAT_MT" \ -l "IMP, IMP-megahit, Naive, MetAmos_MGMT, MOCAT_MGMT, IMP_MG, MetAmos_MG, MOCAT_MG, IMP_MT, MetAmos_MT, MOCAT_MT" \
-f $IMP \ -f $IMP \
$IMP_MEGAHIT \ $IMP_MEGAHIT \
$NAIVE \
$METAMOS \ $METAMOS \
$MOCAT \ $MOCAT \
$IMP_MG \ $IMP_MG \
......
...@@ -13,17 +13,19 @@ MOCAT_MG=$7 ...@@ -13,17 +13,19 @@ MOCAT_MG=$7
IMP_MT=$8 IMP_MT=$8
METAMOS_MT=$9 METAMOS_MT=$9
MOCAT_MT=${10} MOCAT_MT=${10}
NAIVE=${11}
OUTDIR=${11} OUTDIR=${12}
date date
#source ../preload_modules.sh #source ../preload_modules.sh
/mnt/gaiagpfs/projects/ecosystem_biology/local_tools/quast/metaquast.py \ /mnt/gaiagpfs/projects/ecosystem_biology/local_tools/quast/metaquast.py \
-o $OUTDIR -t 12 -f \ -o $OUTDIR -t 12 -f \
-l "IMP, IMP-megahit, MetAmos_MGMT, MOCAT_MGMT, IMP_MG, MetAmos_MG, MOCAT_MG, IMP_MT, MetAmos_MT, MOCAT_MT" \ -l "IMP, IMP-megahit, Naive, MetAmos_MGMT, MOCAT_MGMT, IMP_MG, MetAmos_MG, MOCAT_MG, IMP_MT, MetAmos_MT, MOCAT_MT" \
-R /mnt/nfs/projects/ecosystem_biology/test_datasets/CelajEtAl/73_species/ \ -R /mnt/nfs/projects/ecosystem_biology/test_datasets/CelajEtAl/73_species/ \
${IMP} \ ${IMP} \
${IMP_MEGAHIT} \ ${IMP_MEGAHIT} \
${NAIVE} \
${METAMOS} \ ${METAMOS} \
${MOCAT} \ ${MOCAT} \
${IMP_MG} \ ${IMP_MG} \
......
...@@ -2,31 +2,33 @@ ...@@ -2,31 +2,33 @@
#OARSUB="oarsub --notify "mail:shaman.narayanasamy@uni.lu" -t bigmem -t idempotent -t besteffort -l core=8/nodes=1,walltime=120" #OARSUB="oarsub --notify "mail:shaman.narayanasamy@uni.lu" -t bigmem -t idempotent -t besteffort -l core=8/nodes=1,walltime=120"
#OARSUB="oarsub --notify "mail:shaman.narayanasamy@uni.lu" -l core=12/nodes=1,walltime=48 -t bigmem -t besteffort -t idempotent" #OARSUB="oarsub --notify "mail:shaman.narayanasamy@uni.lu" -l core=12/nodes=1,walltime=48 -t bigmem -t besteffort -t idempotent"
OARSUB="oarsub --notify "mail:shaman.narayanasamy@uni.lu" -l nodes=1,walltime=120" #OARSUB="oarsub --notify "mail:shaman.narayanasamy@uni.lu" -l nodes=1,walltime=120"
OARSUB="oarsub --notify "mail:shaman.narayanasamy@uni.lu" -t bigmem -p "network_address=\'gaia-183\'" --project "project_biocore" -l core=6/nodes=1,walltime=72"
### MGMT assemblies
#IMP="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/SM/Assembly/MGMT.assembly.merged.fa" ## MGMT assemblies
#IMP_MEGAHIT="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/SM_megahit/Assembly/MGMT.assembly.merged.fa" IMP="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/SM/Assembly/MGMT.assembly.merged.fa"
#METAMOS="/scratch/users/snarayanasamy/IMP_MS_data/metAmosAnalysis/SM/MGMT/default/SM/Assemble/out/soapdenovo.31.asm.contig" IMP_MEGAHIT="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/SM_megahit/Assembly/MGMT.assembly.merged.fa"
#MOCAT="/scratch/users/snarayanasamy/IMP_MS_data/MOCAT_analysis/Combined/SM/SM_MOCAT_MGMT" NAIVE="/scratch/users/snarayanasamy/IMP_MS_data/naive_assemblies/SM/MG_MT_cap3.merged.fa"
# METAMOS="/scratch/users/snarayanasamy/IMP_MS_data/metAmosAnalysis/SM/MGMT/default/SM/Assemble/out/soapdenovo.31.asm.contig"
### MG assemblies MOCAT="/scratch/users/snarayanasamy/IMP_MS_data/MOCAT_analysis/Combined/SM/SM_MOCAT_MGMT"
#IMP_MG="/scratch/users/snarayanasamy/IMP_MS_data/iterative_assemblies/MG_assemblies/SM/MG_contigs_merged_2.fa"
#METAMOS_MG="/scratch/users/snarayanasamy/IMP_MS_data/metAmosAnalysis/SM/MG/default/SM/Assemble/out/soapdenovo.31.asm.contig" ## MG assemblies
#MOCAT_MG="/scratch/users/snarayanasamy/IMP_MS_data/MOCAT_analysis/MG/SM/SM_MOCAT_MG" IMP_MG="/scratch/users/snarayanasamy/IMP_MS_data/iterative_assemblies/MG_assemblies/SM/MG_contigs_merged_2.fa"
# METAMOS_MG="/scratch/users/snarayanasamy/IMP_MS_data/metAmosAnalysis/SM/MG/default/SM/Assemble/out/soapdenovo.31.asm.contig"
### MT assemblies MOCAT_MG="/scratch/users/snarayanasamy/IMP_MS_data/MOCAT_analysis/MG/SM/SM_MOCAT_MG"
#IMP_MT="/scratch/users/snarayanasamy/IMP_MS_data/iterative_assemblies/MT_assemblies/SM/MT_contigs_merged_2.fa"
#METAMOS_MT="/scratch/users/snarayanasamy/IMP_MS_data/metAmosAnalysis/SM/MT/default/SM/Assemble/out/soapdenovo.31.asm.contig" ## MT assemblies
#MOCAT_MT="/scratch/users/snarayanasamy/IMP_MS_data/MOCAT_analysis/MT/SM/SM_MOCAT_MT" IMP_MT="/scratch/users/snarayanasamy/IMP_MS_data/iterative_assemblies/MT_assemblies/SM/MT_contigs_merged_2.fa"
# METAMOS_MT="/scratch/users/snarayanasamy/IMP_MS_data/metAmosAnalysis/SM/MT/default/SM/Assemble/out/soapdenovo.31.asm.contig"
#OUTDIR="/scratch/users/snarayanasamy/IMP_MS_data/metaquast_analysis/SM" MOCAT_MT="/scratch/users/snarayanasamy/IMP_MS_data/MOCAT_analysis/MT/SM/SM_MOCAT_MT"
#
#${OARSUB} -n "SM_metaquast" "./execution_SM.sh $IMP $IMP_MEGAHIT $METAMOS $MOCAT $IMP_MG $METAMOS_MG $MOCAT_MG $IMP_MT $METAMOS_MT $MOCAT_MT $OUTDIR" OUTDIR="/scratch/users/snarayanasamy/IMP_MS_data/metaquast_analysis/SM"
#declare -a SAMPLES=("HF1" "HF2" "HF3" "HF4" "HF5" "WW1" "WW2" "WW3" "WW4" "BG") ${OARSUB} -n "SM_metaquast" "./execution_SM.sh $IMP $IMP_MEGAHIT $METAMOS $MOCAT $IMP_MG $METAMOS_MG $MOCAT_MG $IMP_MT $METAMOS_MT $MOCAT_MT $NAIVE $OUTDIR"
declare -a SAMPLES=("HF1" "HF2" "HF3" "HF4" "HF5" "WW1" "WW2" "WW3" "WW4" "BG")
#declare -a SAMPLES=("WW2" "WW3" "WW4") #declare -a SAMPLES=("WW2" "WW3" "WW4")
declare -a SAMPLES=("WW1") #declare -a SAMPLES=("WW1")
## Repeat for all the data sets ## Repeat for all the data sets
for S in "${SAMPLES[@]}" for S in "${SAMPLES[@]}"
...@@ -45,6 +47,7 @@ do ...@@ -45,6 +47,7 @@ do
IMP="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/${S}/Assembly/MGMT.assembly.merged.fa" IMP="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/${S}/Assembly/MGMT.assembly.merged.fa"
IMP_MEGAHIT="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/${S}_megahit/Assembly/MGMT.assembly.merged.fa" IMP_MEGAHIT="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/${S}_megahit/Assembly/MGMT.assembly.merged.fa"
METAMOS="/scratch/users/snarayanasamy/IMP_MS_data/metAmosAnalysis/${S1}/MGMT/default/${S}/Assemble/out/soapdenovo.31.asm.contig" METAMOS="/scratch/users/snarayanasamy/IMP_MS_data/metAmosAnalysis/${S1}/MGMT/default/${S}/Assemble/out/soapdenovo.31.asm.contig"
NAIVE="/scratch/users/snarayanasamy/IMP_MS_data/naive_assemblies/${S}/MG_MT_cap3.merged.fa"
MOCAT="/scratch/users/snarayanasamy/IMP_MS_data/MOCAT_analysis/Combined/${S1}/${S}_MOCAT_MGMT" MOCAT="/scratch/users/snarayanasamy/IMP_MS_data/MOCAT_analysis/Combined/${S1}/${S}_MOCAT_MGMT"
## MG assemblies ## MG assemblies
...@@ -59,5 +62,5 @@ do ...@@ -59,5 +62,5 @@ do
OUTDIR="/scratch/users/snarayanasamy/IMP_MS_data/metaquast_analysis/${S}" OUTDIR="/scratch/users/snarayanasamy/IMP_MS_data/metaquast_analysis/${S}"
${OARSUB} -n "${S}_metaquast" "./execution.sh $IMP $IMP_MEGAHIT $METAMOS $MOCAT $IMP_MG $METAMOS_MG $MOCAT_MG $IMP_MT $METAMOS_MT $MOCAT_MT $OUTDIR" ${OARSUB} -n "${S}_metaquast" "./execution.sh $IMP $IMP_MEGAHIT $METAMOS $MOCAT $IMP_MG $METAMOS_MG $MOCAT_MG $IMP_MT $METAMOS_MT $MOCAT_MT $NAIVE $OUTDIR"
done done
...@@ -16,5 +16,5 @@ INPUT_DIR=$INDIR \ ...@@ -16,5 +16,5 @@ INPUT_DIR=$INDIR \
MG_ASSM=$MG_ASSM \ MG_ASSM=$MG_ASSM \
MT_ASSM=$MT_ASSM \ MT_ASSM=$MT_ASSM \
TMP=$TMPDIR \ TMP=$TMPDIR \
snakemake -pr ALL snakemake $7
date date
...@@ -15,8 +15,8 @@ do ...@@ -15,8 +15,8 @@ do
MT_ASSM="/scratch/users/snarayanasamy/IMP_MS_data/iterative_assemblies/MT_assemblies/${S}/MT_contigs_1.fa" MT_ASSM="/scratch/users/snarayanasamy/IMP_MS_data/iterative_assemblies/MT_assemblies/${S}/MT_contigs_1.fa"
TMPDIR="/scratch/users/snarayanasamy/IMP_MS_data/naive_assemblies/${S}/tmp" TMPDIR="/scratch/users/snarayanasamy/IMP_MS_data/naive_assemblies/${S}/tmp"
${OARSUB} -n "${S}_naive_assm" "./execution.sh $INDIR $OUTDIR $OUTLOG $MG_ASSM $MT_ASSM $TMPDIR" #${OARSUB} -n "${S}_naive_assm" "./execution.sh $INDIR $OUTDIR $OUTLOG $MG_ASSM $MT_ASSM $TMPDIR"
#CMD="./execution.sh $INDIR $OUTDIR $OUTLOG $MG_ASSM $MT_ASSM $TMPDIR" CMD="./execution.sh $INDIR $OUTDIR $OUTLOG $MG_ASSM $MT_ASSM $TMPDIR"
echo $CMD echo $CMD
# exec ${CMD} # exec ${CMD}
......
#!/bin/bash -l
#OARSUB="oarsub --notify "mail:shaman.narayanasamy@uni.lu" -t bigsmp -t idempotent -t besteffort -l core=12/nodes=1,walltime=120"
OARSUB="oarsub --notify "mail:shaman.narayanasamy@uni.lu" -t bigmem -t idempotent -t besteffort -l core=2/nodes=1,walltime=72"
declare -a SAMPLES=("SM" "HF1" "HF2" "HF3" "HF4" "HF5" "WW1" "WW2" "WW3" "WW4" "BG")
### Repeat for all the data sets
for S in "${SAMPLES[@]}"
do
NAIVE_REF="/scratch/users/snarayanasamy/IMP_MS_data/naive_assemblies/${S}"
OUTDIR="/scratch/users/snarayanasamy/IMP_MS_data/prodigal_analysis/naive_assemblies/${S}"
${OARSUB} -n "${S}_naive_prodigal" "./makeGenePredictionsProdigal.sh $NAIVE_REF $OUTDIR"
done
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