https://bioinformaticsonline.com/snippets/view/37486/running-reapr? https://bioinformaticsonline.com/snippets/view/37486/running-reapr Mon, 06 Aug 2018 08:24:15 -0500 https://bioinformaticsonline.com/snippets/view/37486/running-reapr set -e echo "Running reapr version 1.0.18 pipeline:" echo "/home/urbe/Tools/Reapr_1.0.18/reapr WadinetaGapFilled.gapfilled.iteration1.fa out.smaltmap.bam out.pipeline perfect" echo "[REAPR pipeline] Running facheck" echo "/home/urbe/Tools/Reapr_1.0.18/reapr facheck WadinetaGapFilled.gapfilled.iteration1.fa" echo "[REAPR pipeline] Running preprocess" echo "/home/urbe/Tools/Reapr_1.0.18/reapr preprocess WadinetaGapFilled.gapfilled.iteration1.fa out.smaltmap.bam out.pipeline" cd out.pipeline echo "[REAPR pipeline] Running stats" echo "/home/urbe/Tools/Reapr_1.0.18/reapr stats -p /home/urbe/Tools/Reapr_1.0.18/Wadineta_Afasta_gapfilled_genome/perfect.perfect_cov.gz ./ 01.stats" echo "[REAPR pipeline] Running fcdrate" /home/urbe/Tools/Reapr_1.0.18/reapr fcdrate ./ 01.stats 02.fcdrate fcdcutoff=`tail -n 1 02.fcdrate.info.txt | cut -f 1` echo "[REAPR pipeline] Running score" /home/urbe/Tools/Reapr_1.0.18/reapr score -P 5 00.assembly.fa.gaps.gz 00.in.bam 01.stats $fcdcutoff 03.score echo "[REAPR pipeline] Running break" /home/urbe/Tools/Reapr_1.0.18/reapr break 00.assembly.fa 03.score.errors.gff.gz 04.break echo "[REAPR pipeline] Running summary" /home/urbe/Tools/Reapr_1.0.18/reapr summary 00.assembly.fa 03.score 04.break 05.summary -------- set -e echo "Running reapr version 1.0.18 pipeline:" echo "/home/urbe/Tools/Reapr_1.0.18/reapr WadinetaGapFilled.gapfilled.iteration1.fa out.smaltmap.bam out.pipeline perfect" echo "[REAPR pipeline] Running facheck" /home/urbe/Tools/Reapr_1.0.18/reapr facheck WadinetaGapFilled.gapfilled.iteration1.fa echo "[REAPR pipeline] Running preprocess" /home/urbe/Tools/Reapr_1.0.18/reapr preprocess WadinetaGapFilled.gapfilled.iteration1.fa out.smaltmap.bam out.pipeline cd out.pipeline echo "[REAPR pipeline] Running stats" /home/urbe/Tools/Reapr_1.0.18/reapr stats -p /home/urbe/Tools/Reapr_1.0.18/Wadineta_Afasta_gapfilled_genome/perfect.perfect_cov.gz ./ 01.stats echo "[REAPR pipeline] Running fcdrate" /home/urbe/Tools/Reapr_1.0.18/reapr fcdrate ./ 01.stats 02.fcdrate fcdcutoff=`tail -n 1 02.fcdrate.info.txt | cut -f 1` echo "[REAPR pipeline] Running score" /home/urbe/Tools/Reapr_1.0.18/reapr score -P 5 00.assembly.fa.gaps.gz 00.in.bam 01.stats $fcdcutoff 03.score echo "[REAPR pipeline] Running break" /home/urbe/Tools/Reapr_1.0.18/reapr break 00.assembly.fa 03.score.errors.gff.gz 04.break echo "[REAPR pipeline] Running summary" /home/urbe/Tools/Reapr_1.0.18/reapr summary 00.assembly.fa 03.score 04.break 05.summary ----- #!/usr/bin/env bash set -e echo " test smaltmap " reapr smaltmap -u 5 -n 25 WadinetaGapFilled.gapfilled.iteration1.fa /home/urbe/DATA/OriginalReads/ANature/GC027568.151120_Adineta_Nature_and_Habrotrocha.160226.HiSeq2000.FCB.lane1.gcap_dev.R1.fastq /home/urbe/DATA/OriginalReads/ANature/GC027568.151120_Adineta_Nature_and_Habrotrocha.160226.HiSeq2000.FCB.lane1.gcap_dev.R2.fastq out.smaltmap.bam echo " smaltmap OK ______________________________________________________________________________ test perfectmap " reapr perfectmap WadinetaGapFilled.gapfilled.iteration1.fa /home/urbe/DATA/OriginalReads/ANature/GC027568.151120_Adineta_Nature_and_Habrotrocha.160226.HiSeq2000.FCB.lane1.gcap_dev.R1.fastq /home/urbe/DATA/OriginalReads/ANature/GC027568.151120_Adineta_Nature_and_Habrotrocha.160226.HiSeq2000.FCB.lane1.gcap_dev.R2.fastq 165 out.perfectmap echo " perfectmap OK ______________________________________________________________________________ test pipeline " reapr pipeline WadinetaGapFilled.gapfilled.iteration1.fa out.smaltmap.bam out.pipeline perfect echo " pipeline OK ______________________________________________________________________________ All looked OK so cleaning files... " #rm -fr out.* echo " All done! "]]> Jit