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added scripts to use metaphlan vith VSCs and profile metagenomes
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| Original file line number | Diff line number | Diff line change |
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| #!/bin/bash | ||
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| #PBS -l place=free | ||
| #PBS -V | ||
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| DBF=/shares/CIBIO-Storage/CM/scratch/users/moreno.zolfo/virome_data/mp3_release/VSC5_MP3/database/release_01 | ||
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| if [ ! $ncores ]; then ncores="2"; fi; | ||
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| ldn=${dn//"/"/"__"}; | ||
| NODE_TEMPFOLDER=/tmp/ | ||
| SERVER_TEMPFOLDER=/shares/CIBIO-Storage/CM/tmp/mzolfo/tmp_data/ | ||
| SERVER_BASEFOLDER=/shares/CIBIO-Storage/CM/scratch/users/moreno.zolfo/virome_data/prevalence4/${ldn}/ | ||
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| FREESPACE=$(df --output=avail $NODE_TEMPFOLDER | tail -n1); | ||
| WORKSIZE=$(du -L -ck ${prefix}/${dn}/reads/${fn}/*${extension} | tail -n1 | cut -f1) | ||
| REQSIZE=$((WORKSIZE*6)) | ||
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| if [[ $FREESPACE -lt $REQSIZE ]]; then | ||
| TEMPFOLDER=${SERVER_TEMPFOLDER}/MP3_${ldn}___${fn}; | ||
| else | ||
| TEMPFOLDER=${NODE_TEMPFOLDER}/MP3_${ldn}___${fn}; | ||
| fi | ||
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| if [ -d ${TEMPFOLDER} ]; then rm -r ${TEMPFOLDER}/; fi; | ||
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| mkdir -p $TEMPFOLDER/ | ||
| mkdir -p $SERVER_BASEFOLDER/ | ||
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| $uncompress_cmd ${prefix}/${dn}/reads/${fn}/*${extension} | metaphlan --input_type fastq --bowtie2db ${DBF} -x mpa_v30_CHOCOPhlAn_201901_vsc --profile_vsc --vsc_out ${TEMPFOLDER}/${fn}.vsc.tsv --nproc ${ncores} --bowtie2out ${TEMPFOLDER}/${fn}.bowtie.bz2 > ${TEMPFOLDER}/${fn}.profile.tsv | ||
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| mv ${TEMPFOLDER}/*.tsv ${SERVER_BASEFOLDER}/; | ||
| rm ${SERVER_BASEFOLDER}/${dn}__${fn}.wk | ||
| rm -r ${TEMPFOLDER}; | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,109 @@ | ||
| #!/bin/bash | ||
| curDir=$(realpath $(dirname $0)); | ||
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| source ${curDir}/workunit_data.sh | ||
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| ############################################## | ||
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| mode=$1; | ||
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| if [ $mode == "U" ]; then | ||
| extension='.fastq' | ||
| extraction_cmd='cat' | ||
| fi; | ||
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| if [ $mode == "bzip" ]; then | ||
| extension='.fastq.bz2' | ||
| extraction_cmd='bzcat' | ||
| fi; | ||
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| if [ $mode == "gzip" ]; then | ||
| extension='.fastq.gz' | ||
| extraction_cmd='zcat' | ||
| fi; | ||
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| if [ $mode == "fqgz" ]; then | ||
| extension='.fq.gz' | ||
| extraction_cmd='zcat' | ||
| fi; | ||
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| for et in $etp; do | ||
| for utp in $(find ${prefix}/${et}/reads -maxdepth 1 -mindepth 1 -type d); do | ||
| e+=($utp); | ||
| done; | ||
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| mkdir -p ${logFolder}/${et}/; | ||
| mkdir -p ${odir}/${et}/ | ||
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| done; | ||
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| while true; do | ||
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| bt=0; | ||
| b_short=$(qstat -u moreno.zolfo | grep short | grep "VDBP" | wc -l); | ||
| b_common=$(qstat -u moreno.zolfo | grep common | grep "VDBP" | wc -l); | ||
| b_cibio=$(qstat -u moreno.zolfo | grep CIBIO_ | grep "VDBP" | wc -l); | ||
| b_cibiocm=$(qstat -u moreno.zolfo | grep CIBIOCM | grep "VDBP" | wc -l); | ||
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| for folder in ${e[@]}; do | ||
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| sample=$(basename $folder); | ||
| dataset=$(basename $(dirname $(dirname $folder))); | ||
| odirE=${odir}/${dataset}/ | ||
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| if [ ! -f ${odir}/${dataset}/${sample}.vsc.tsv ] && [ ! -f ${odir}/${dataset}/${dataset}__${sample}.wk ]; then | ||
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| if [ $b_short -lt 30 ]; then | ||
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| echo "QUEUE (short)" ${dataset} ${sample}; | ||
| qsub -q short_cpuQ -v prefix=\"${base}\",dn=\"${dataset}\",fn=\"${sample}\",uncompress_cmd=\"${extraction_cmd}\",extension=\"${extension}\",ncores=\"8\" -N VDBP_${dataset}_${sample} -o ${logFolder}/${dataset}/VDBP_${dataset}_${sample}.o.log -e ${logFolder}/${dataset}/VDBP_${dataset}_${sample}.e.log -l select=1:ncpus=8 ${curDir}/launch_vir.sh; | ||
| touch ${odir}/${dataset}/${dataset}__${sample}.wk | ||
| b_short=$((b_short+1)); | ||
| bt=$((bt+1)); | ||
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| elif [ $b_common -lt 60 ]; then | ||
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| echo "QUEUE (common)" ${dataset} ${sample}; | ||
| qsub -q common_cpuQ -v prefix=\"${base}\",dn=\"${dataset}\",fn=\"${sample}\",uncompress_cmd=\"${extraction_cmd}\",extension=\"${extension}\",ncores=\"2\" -N VDBP_${dataset}_${sample} -o ${logFolder}/${dataset}/VDBP_${dataset}_${sample}.o.log -e ${logFolder}/${dataset}/VDBP_${dataset}_${sample}.e.log -l select=1:ncpus=2 ${curDir}/launch_vir.sh; | ||
| touch ${odir}/${dataset}/${dataset}__${sample}.wk | ||
| b_common=$((b_common+1)); | ||
| bt=$((bt+1)); | ||
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| elif [ $b_cibio -lt 25 ]; then | ||
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| echo "QUEUE (common)" ${dataset} ${sample}; | ||
| qsub -q CIBIO_cpuQ -v prefix=\"${base}\",dn=\"${dataset}\",fn=\"${sample}\",uncompress_cmd=\"${extraction_cmd}\",extension=\"${extension}\",ncores=\"2\" -N VDBP_${dataset}_${sample} -o ${logFolder}/${dataset}/VDBP_${dataset}_${sample}.o.log -e ${logFolder}/${dataset}/VDBP_${dataset}_${sample}.e.log -l select=1:ncpus=2 ${curDir}/launch_vir.sh; | ||
| touch ${odir}/${dataset}/${dataset}__${sample}.wk | ||
| b_cibio=$((b_cibio+1)); | ||
| bt=$((bt+1)); | ||
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| elif [ $b_cibiocm -lt 25 ]; then | ||
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| echo "QUEUE (common)" ${dataset} ${sample}; | ||
| qsub -q CIBIOCM_cpuQ -v prefix=\"${base}\",dn=\"${dataset}\",fn=\"${sample}\",uncompress_cmd=\"${extraction_cmd}\",extension=\"${extension}\",ncores=\"2\" -N VDBP_${dataset}_${sample} -o ${logFolder}/${dataset}/VDBP_${dataset}_${sample}.o.log -e ${logFolder}/${dataset}/VDBP_${dataset}_${sample}.e.log -l select=1:ncpus=2 ${curDir}/launch_vir.sh; | ||
| touch ${odir}/${dataset}/${dataset}__${sample}.wk | ||
| b_cibiocm=$((b_cibiocm+1)); | ||
| bt=$((bt+1)); | ||
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| fi; | ||
| # else | ||
| # echo "SKIP" ${dataset} ${sample}; | ||
| fi; | ||
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| done; | ||
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| a=$(qstat -u moreno.zolfo | grep "VDBP" | grep " R " | wc -l); | ||
| q=$(qstat -u moreno.zolfo | grep "VDBP" | grep " Q " | wc -l); | ||
| ete=${#e[@]} | ||
| ft=$(find ${odir}/ -name "*.vsc.tsv" | wc -l); | ||
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| tg=#$(($ete-$ft)); | ||
| echo $(date) "| " $bt "jobs launched, " $a "running ", $q "queued " $tg" to go. See you in one minute." ; | ||
| sleep 60 | ||
| b=0; | ||
| done; |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,71 @@ | ||
| #!/bin/bash | ||
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| odir="/shares/CIBIO-Storage/CM/scratch/users/moreno.zolfo/virome_data/prevalence4/"; | ||
| logFolder="/shares/CIBIO-Storage/CM/scratch/users/moreno.zolfo/virome_data/prevalence4/scripts/logs"; | ||
| prefix="/shares/CIBIO-Storage/CM/cmstore/data/meta" | ||
| base=$prefix; | ||
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| etp='HMP_2012 | ||
| LiuB_2012 | ||
| BengtssonPalmeJ_2015 | ||
| PiperHG_2016 | ||
| ContevilleLC_2019 | ||
| GopalakrishnanV_2018 | ||
| RosaBA_2018 | ||
| KieserS_2018 | ||
| LassalleF_2017 | ||
| SankaranarayananK_2015 | ||
| RampelliS_2015 | ||
| MatsonV_2018 | ||
| SmitsSA_2017 | ||
| WingleeK_2017 | ||
| LomanNJ_2013 | ||
| OlmMR_2017 | ||
| LawrenceA_2015 | ||
| GeversD_2014 | ||
| Heitz-BuschartA_2016 | ||
| LiSS_2016 | ||
| LokmerA_2019 | ||
| Obregon-TitoAJ_2015 | ||
| GuptaA_2019 | ||
| WampachL_2018 | ||
| VoigtAY_2015 | ||
| RaymondF_2016 | ||
| YeZ_2018 | ||
| KorpelaK_2016 | ||
| ThomasAM_2019_c | ||
| HanniganGD_2017 | ||
| LoombaR_2017 | ||
| LouisS_2016 | ||
| ChengpingW_2017 | ||
| IjazUZ_2017 | ||
| ChuDM_2017 | ||
| DhakanDB_2019 | ||
| LiuW_2016 | ||
| VogtmannE_2016 | ||
| HeQ_2017 | ||
| KosticAD_2015 | ||
| WirbelJ_2018 | ||
| YuJ_2015 | ||
| KarlssonFH_2013 | ||
| FengQ_2015 | ||
| ZellerG_2014 | ||
| WenC_2017 | ||
| LiJ_2017 | ||
| HansenLBS_2018 | ||
| VincentC_2016 | ||
| QinN_2014 | ||
| XieH_2016 | ||
| LiJ_2014 | ||
| HallAB_2017 | ||
| CosteaPI_2017 | ||
| PehrssonE_2016 | ||
| YassourM_2018 | ||
| LeChatelierE_2013 | ||
| QinJ_2012 | ||
| JieZ_2017 | ||
| NielsenHB_2014 | ||
| BackhedF_2015 | ||
| SchirmerM_2016 | ||
| VatanenT_2016 | ||
| YachidaS_2019'; |