Add new launcher and modify execution and launcher scripts

metaquast_analysis/execution.sh

@@ -13,16 +13,18 @@ MOCAT_MG=$7
 IMP_MT=$8
 METAMOS_MT=$9
 MOCAT_MT=${10}
+NAIVE=${11}
 
-OUTDIR=${11}
+OUTDIR=${12}
 
 date
 #source ../preload_modules.sh
 /mnt/gaiagpfs/projects/ecosystem_biology/local_tools/quast/metaquast.py \
-    -o $OUTDIR -t 12 \
-    -l "IMP, IMP-megahit, MetAmos_MGMT, MOCAT_MGMT, IMP_MG, MetAmos_MG, MOCAT_MG, IMP_MT, MetAmos_MT, MOCAT_MT" \
+    -o $OUTDIR -t 6 \
+    -l "IMP, IMP-megahit, Naive, MetAmos_MGMT, MOCAT_MGMT, IMP_MG, MetAmos_MG, MOCAT_MG, IMP_MT, MetAmos_MT, MOCAT_MT" \
     -f $IMP \
     $IMP_MEGAHIT \
+    $NAIVE \
     $METAMOS \
     $MOCAT \
     $IMP_MG \

metaquast_analysis/execution_SM.sh

@@ -13,17 +13,19 @@ MOCAT_MG=$7
 IMP_MT=$8
 METAMOS_MT=$9
 MOCAT_MT=${10}
+NAIVE=${11}
 
-OUTDIR=${11}
+OUTDIR=${12}
 
 date
 #source ../preload_modules.sh
 /mnt/gaiagpfs/projects/ecosystem_biology/local_tools/quast/metaquast.py \
     -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/ \
     ${IMP} \
     ${IMP_MEGAHIT} \
+    ${NAIVE} \
     ${METAMOS} \
     ${MOCAT} \
     ${IMP_MG} \

metaquast_analysis/launcher.sh

@@ -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" -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"
-
-### MGMT assemblies
-#IMP="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/SM/Assembly/MGMT.assembly.merged.fa"
-#IMP_MEGAHIT="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/SM_megahit/Assembly/MGMT.assembly.merged.fa"
-#METAMOS="/scratch/users/snarayanasamy/IMP_MS_data/metAmosAnalysis/SM/MGMT/default/SM/Assemble/out/soapdenovo.31.asm.contig"
-#MOCAT="/scratch/users/snarayanasamy/IMP_MS_data/MOCAT_analysis/Combined/SM/SM_MOCAT_MGMT"
-#
-### MG assemblies
-#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"
-#MOCAT_MG="/scratch/users/snarayanasamy/IMP_MS_data/MOCAT_analysis/MG/SM/SM_MOCAT_MG"
-#
-### MT assemblies
-#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"
-#MOCAT_MT="/scratch/users/snarayanasamy/IMP_MS_data/MOCAT_analysis/MT/SM/SM_MOCAT_MT"
-#
-#OUTDIR="/scratch/users/snarayanasamy/IMP_MS_data/metaquast_analysis/SM"
-#
-#${OARSUB} -n "SM_metaquast" "./execution_SM.sh $IMP $IMP_MEGAHIT $METAMOS $MOCAT $IMP_MG $METAMOS_MG $MOCAT_MG $IMP_MT $METAMOS_MT $MOCAT_MT $OUTDIR"
-
-#declare -a SAMPLES=("HF1" "HF2" "HF3" "HF4" "HF5" "WW1" "WW2" "WW3" "WW4" "BG")
+#OARSUB="oarsub --notify "mail:shaman.narayanasamy@uni.lu" -l nodes=1,walltime=120"
+OARSUB="oarsub --notify "mail:shaman.narayanasamy@uni.lu" -t bigmem -p "network_address=\'gaia-183\'" --project "project_biocore" -l core=6/nodes=1,walltime=72"
+
+## MGMT assemblies
+IMP="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/SM/Assembly/MGMT.assembly.merged.fa"
+IMP_MEGAHIT="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/SM_megahit/Assembly/MGMT.assembly.merged.fa"
+NAIVE="/scratch/users/snarayanasamy/IMP_MS_data/naive_assemblies/SM/MG_MT_cap3.merged.fa"
+METAMOS="/scratch/users/snarayanasamy/IMP_MS_data/metAmosAnalysis/SM/MGMT/default/SM/Assemble/out/soapdenovo.31.asm.contig"
+MOCAT="/scratch/users/snarayanasamy/IMP_MS_data/MOCAT_analysis/Combined/SM/SM_MOCAT_MGMT"
+
+## MG assemblies
+IMP_MG="/scratch/users/snarayanasamy/IMP_MS_data/iterative_assemblies/MG_assemblies/SM/MG_contigs_merged_2.fa"
+METAMOS_MG="/scratch/users/snarayanasamy/IMP_MS_data/metAmosAnalysis/SM/MG/default/SM/Assemble/out/soapdenovo.31.asm.contig"
+MOCAT_MG="/scratch/users/snarayanasamy/IMP_MS_data/MOCAT_analysis/MG/SM/SM_MOCAT_MG"
+
+## MT assemblies
+IMP_MT="/scratch/users/snarayanasamy/IMP_MS_data/iterative_assemblies/MT_assemblies/SM/MT_contigs_merged_2.fa"
+METAMOS_MT="/scratch/users/snarayanasamy/IMP_MS_data/metAmosAnalysis/SM/MT/default/SM/Assemble/out/soapdenovo.31.asm.contig"
+MOCAT_MT="/scratch/users/snarayanasamy/IMP_MS_data/MOCAT_analysis/MT/SM/SM_MOCAT_MT"
+
+OUTDIR="/scratch/users/snarayanasamy/IMP_MS_data/metaquast_analysis/SM"
+
+${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=("WW1")
+#declare -a SAMPLES=("WW1")
 
 ## Repeat for all the data sets
 for S in "${SAMPLES[@]}" 
@@ -45,6 +47,7 @@ do
     IMP="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/${S}/Assembly/MGMT.assembly.merged.fa"
     IMP_MEGAHIT="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/${S}_megahit/Assembly/MGMT.assembly.merged.fa"
     METAMOS="/scratch/users/snarayanasamy/IMP_MS_data/metAmosAnalysis/${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"
 
     ## MG assemblies
@@ -59,5 +62,5 @@ do
 
     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

naive_assembly/execution.sh

@@ -16,5 +16,5 @@ INPUT_DIR=$INDIR \
   MG_ASSM=$MG_ASSM \
   MT_ASSM=$MT_ASSM \
   TMP=$TMPDIR \
-  snakemake -pr ALL
+  snakemake $7
 date 

naive_assembly/launcher.sh

@@ -15,8 +15,8 @@ do
     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"
     
-    ${OARSUB} -n "${S}_naive_assm" "./execution.sh $INDIR $OUTDIR $OUTLOG $MG_ASSM $MT_ASSM $TMPDIR"
-    #CMD="./execution.sh $INDIR $OUTDIR $OUTLOG $MG_ASSM $MT_ASSM $TMPDIR"
+    #${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"
 
     echo $CMD
 #    exec ${CMD}

prodigal_analysis/launcher_naive.sh

+#!/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