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!
"
