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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,166 @@ | ||
| ## Polish contigs with Racon | ||
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||
| out=$1 | ||
| name=$2 | ||
| data=$3 | ||
| pwd=$4 | ||
| threads=$5 | ||
| RAM=$6 | ||
| racon=$7 | ||
| decont=$8 | ||
|
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||
| printf "sh FullPipeline/racon.sh $1 $2 $3 $4 $5 $6 $7 $8\n# " | ||
|
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| if [[ $data == *'ILL'* ]] | ||
| then | ||
| if [[ $decont == 'no' ]] | ||
| then | ||
| IllInp1=${name}_1_val_1 | ||
| IllInp2=${name}_2_val_2 | ||
| else | ||
| IllInp1=kraken_illumina_${name}_1 | ||
| IllInp2=kraken_illumina_${name}_2 | ||
| fi | ||
| fi | ||
|
|
||
| if [[ $data == *'ONT'* ]] | ||
| then | ||
| if [[ $decont == 'no' ]] | ||
| then | ||
| OntInp=${name}_ont | ||
| else | ||
| OntInp=raken_ont_${name} | ||
| fi | ||
| fi | ||
|
|
||
| if [[ $data == *'PB'* ]] | ||
| then | ||
| if [[ $decont == 'no' ]] | ||
| then | ||
| PbInp=${name}_pb | ||
| else | ||
| PbInp=raken_${name}_pb | ||
| fi | ||
| fi | ||
|
|
||
| ############################# | ||
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| mkdir -p ${out}/results/Racon | ||
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| echo """ | ||
| #!/bin/sh | ||
| ## name of Job | ||
| #PBS -N Racon_${name} | ||
| ## Redirect output stream to this file. | ||
| #PBS -o ${out}/log/Racon_${name}_log.txt | ||
| ## Stream Standard Output AND Standard Error to outputfile (see above) | ||
| #PBS -j oe | ||
| ## Select ${threads} cores and ${RAM}gb of RAM | ||
| #PBS -l select=1:ncpus=${threads}:mem=${RAM}g | ||
| ######## load dependencies ####### | ||
| source /opt/anaconda3/etc/profile.d/conda.sh | ||
| module load NGSmapper/minimap2-2.17 | ||
| conda activate racon_1.5.0 | ||
| conda activate medaka-1.4.4 | ||
| ######## run analyses ####### | ||
| ## Go to pwd | ||
| cd ${pwd} | ||
| ## concatenate Illumina data (if needed) | ||
| if [[ $data == 'ILL' ]] | ||
| then | ||
| gunzip -c ${out}/data/Illumina/${IllInp1}.fq.gz \ | ||
| | sed 's/ 1:.*/\/1/g' \ | ||
| | gzip > ${out}/results/Racon/Ill.fq.gz | ||
| gunzip -c ${out}/data/Illumina/${IllInp2}.fq.gz \ | ||
| | sed 's/ 2:.*/\/2/g' \ | ||
| | gzip >> ${out}/results/Racon/Ill.fq.gz | ||
| fi | ||
| ## make copy of unpolished contigs | ||
| cp ${out}/output/${name}_${data}.fa ${out}/output/${name}_${data}_unpolished.fa | ||
| pigz ${out}/output/${name}_${data}_unpolished.fa | ||
| ## do Racon polishing | ||
| for (( i=1; i<=${racon}; i++ )) | ||
| do | ||
| if [[ $data == 'ILL' ]] | ||
| then | ||
| minimap2 \ | ||
| -x sr \ | ||
| -t ${threads} \ | ||
| ${out}/output/${name}_${data}.fa \ | ||
| ${out}/results/Racon/Ill.fq.gz \ | ||
| > ${out}/results/Racon/temp_reads_to_draft.paf | ||
| racon \ | ||
| -t ${threads} \ | ||
| ${out}/results/Racon/Ill.fq.gz \ | ||
| ${out}/results/Racon/temp_reads_to_draft.paf \ | ||
| ${out}/output/${name}_${data}.fa \ | ||
| > ${out}/results/Racon/temp_draft_new.fa | ||
| elif [[ $data == *'ONT'* ]] | ||
| then | ||
| minimap2 \ | ||
| -x map-ont \ | ||
| -t ${threads} \ | ||
| ${out}/output/${name}_${data}.fa \ | ||
| ${out}/data/ONT/${OntInp}.fq.gz \ | ||
| > ${out}/results/Racon/temp_reads_to_draft.paf | ||
| racon \ | ||
| -t ${threads} \ | ||
| ${out}/data/ONT/${OntInp}.fq.gz \ | ||
| ${out}/results/Racon/temp_reads_to_draft.paf \ | ||
| ${out}/output/${name}_${data}.fa \ | ||
| > ${out}/results/Racon/temp_draft_new.fa | ||
| else | ||
| minimap2 \ | ||
| -x map-pb \ | ||
| -t ${threads} \ | ||
| ${out}/output/${name}_${data}.fa \ | ||
| ${out}/data/PB/${PbInp}.fq.gz \ | ||
| > ${out}/results/Racon/temp_reads_to_draft.paf | ||
| racon \ | ||
| -t ${threads} \ | ||
| ${out}/data/PB/${PbInp}.fq.gz \ | ||
| ${out}/results/Racon/temp_reads_to_draft.paf \ | ||
| ${out}/output/${name}_${data}.fa | ||
| > ${out}/results/Racon/temp_draft_new.fa | ||
| fi | ||
| mv ${out}/results/Racon/temp_draft_new.fa ${out}/output/${name}_${data}.fa | ||
| done | ||
| if [[ $data == 'ILL' ]] | ||
| then | ||
| rm -f ${out}/results/Racon/Ill.fq.gz | ||
| fi | ||
| """ > ${out}/shell/qsub_racon_${name}.sh | ||
|
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||
| qsub -W block=true ${out}/shell/qsub_racon_${name}.sh |
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