launcher.sh 3.77 KB
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#!/bin/bash -l

#OARSUB="oarsub --notify "mail:shaman.narayanasamy@uni.lu" -t bigmem -t idempotent -t besteffort -l core=8/nodes=1,walltime=120"
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#OARSUB="oarsub --notify "mail:shaman.narayanasamy@uni.lu" -l core=12/nodes=1,walltime=48 -t bigmem -t besteffort -t idempotent"
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#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")
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#declare -a SAMPLES=("WW2" "WW3" "WW4")
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#declare -a SAMPLES=("WW1")
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## Repeat for all the data sets
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for S in "${SAMPLES[@]}" 
do
 check=${#S}
  echo $check
  if [ $check -eq 3 ]
  then 
    S1="${S::-1}"
    echo "$S1" 
  else 
    S1="$S"
    echo "Continue"
  fi
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    ## MGMT assemblies
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    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"
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    NAIVE="/scratch/users/snarayanasamy/IMP_MS_data/naive_assemblies/${S}/MG_MT_cap3.merged.fa"
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    MOCAT="/scratch/users/snarayanasamy/IMP_MS_data/MOCAT_analysis/Combined/${S1}/${S}_MOCAT_MGMT"

    ## MG assemblies
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    IMP_MG="/scratch/users/snarayanasamy/IMP_MS_data/iterative_assemblies/MG_assemblies/${S}/MG_contigs_merged_2.fa"
    METAMOS_MG="/scratch/users/snarayanasamy/IMP_MS_data/metAmosAnalysis/${S1}/MG/default/${S}/Assemble/out/soapdenovo.31.asm.contig"
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    MOCAT_MG="/scratch/users/snarayanasamy/IMP_MS_data/MOCAT_analysis/MG/${S1}/${S}_MOCAT_MG"

    ## MT assemblies
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    IMP_MT="/scratch/users/snarayanasamy/IMP_MS_data/iterative_assemblies/MT_assemblies/${S}/MT_contigs_merged_2.fa"
    METAMOS_MT="/scratch/users/snarayanasamy/IMP_MS_data/metAmosAnalysis/${S1}/MT/default/${S}/Assemble/out/soapdenovo.31.asm.contig"
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    MOCAT_MT="/scratch/users/snarayanasamy/IMP_MS_data/MOCAT_analysis/MT/${S1}/${S}_MOCAT_MT"
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    OUTDIR="/scratch/users/snarayanasamy/IMP_MS_data/metaquast_analysis/${S}"
    
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    ${OARSUB} -n "${S}_metaquast" "./execution.sh $IMP $IMP_MEGAHIT $METAMOS $MOCAT $IMP_MG $METAMOS_MG $MOCAT_MG $IMP_MT $METAMOS_MT $MOCAT_MT $NAIVE $OUTDIR"
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done