Commit 90d266d1 authored by peguerin's avatar peguerin
Browse files

mitoZ factorized

parent 5b43a47e
## softwares/scripts
EXTRACT_FQ_SEQ=`echo "python3 //media/bigvol/peguerin/extractfq/extractfq/extractfq.py"`
## data files
RAWFQGZ1="/media/bigvol/peguerin/170721_SNK268_B_L006_JFP-1_R1.fastq.gz"
RAWFQGZ2="/media/bigvol/peguerin/170721_SNK268_B_L006_JFP-1_R2.fastq.gz"
#RAWFQGZ1="/media/bigvol/peguerin/170721_SNK268_B_L006_JFP-1_R1.fastq.gz"
#RAWFQGZ2="/media/bigvol/peguerin/170721_SNK268_B_L006_JFP-1_R2.fastq.gz"
RAWFQGZ1=$1
RAWFQGZ2=$2
FOLDERRAW=$3
mkdir $FOLDERRAW
##extract 5 Go
mkdir 02-raw
$EXTRACT_FQ_SEQ -fq1 $RAWFQGZ1 -fq2 $RAWFQGZ2 -outfq1 02-raw/raw.1.fq -outfq2 02-raw/raw.2.fq -size_required 5
$EXTRACT_FQ_SEQ -fq1 $RAWFQGZ1 -fq2 $RAWFQGZ2 -outfq1 $FOLDERRAW"/raw.1.fq" -outfq2 $FOLDERRAW"/raw.2.fq" -size_required 5
## softwares/scripts
MITOZ="/media/bigvol/peguerin/MitoZ.simg"
## data files
RAWFQGZ1="02-raw/raw.1.fq"
RAWFQGZ2="02-raw/raw.2.fq"
$MITOZ all --genetic_code 2 --clade Chordata --outprefix mito_mullus \
RAWFQGZ1=$1"/raw.1.fq"
RAWFQGZ2=$1"/raw.2.fq"
OUTPREFIX=$2
## run mitoz
$MITOZ all2 --genetic_code 2 --clade Chordata --outprefix $OUTPREFIX \
--thread_number 64 \
--fastq1 $RAWFQGZ1 \
--fastq2 $RAWFQGZ2 \
......
......@@ -2,24 +2,26 @@
MITOZ="/home/pguerin/working/intrapop/projets/assemble_mitogenome/MitoZ.simg"
EXTRACT_FQ_SEQ=`echo "python3 /home/pguerin/working/intrapop/projets/assemble_mitogenome/extractfq/extractfq/extractfq.py"`
## data files
RAWFQGZ1="/donnees/RESERVEBENEFIT/whole_genome_sequencing/wgs_mullus/JFP-1-2_pairedend/data/fasteris/170721_SNK268_B_L006_JFP-1_R1.fastq.gz"
RAWFQGZ2="/donnees/RESERVEBENEFIT/whole_genome_sequencing/wgs_mullus/JFP-1-2_pairedend/data/fasteris/170721_SNK268_B_L006_JFP-1_R2.fastq.gz"
#### mullus surmuletus
RAWFQGZ1="/media/bigvol/peguerin/170721_SNK268_B_L006_JFP-1_R1.fastq.gz"
RAWFQGZ2="/media/bigvol/peguerin/170721_SNK268_B_L006_JFP-1_R2.fastq.gz"
FOLDERRAW="/media/bigvol/peguerin/raw_mullus/"
OUTPREFIX="mullus_mitoz"
#### diplodus sargus
RAWFQGZ1="goodlength_goodqual_170106_SNK268_A_L006_GWM-869_R1.fastq.gz"
RAWFQGZ2="goodlength_goodqual_170106_SNK268_A_L006_GWM-869_R2.fastq.gz"
FOLDERRAW="/media/bigvol/peguerin/raw_diplodus/"
OUTPREFIX="diplodus_mitoz"
#### serranus cabrilla
RAWFQGZ1="180802_NB501473_A_L1-4_ANIZ-1_R1.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq.gz"
RAWFQGZ2="180802_NB501473_A_L1-4_ANIZ-1_R2.RD30.NotEmpty.LinkerTrimmed-50bp-PR.fastq.gz"
FOLDERRAW="/media/bigvol/peguerin/raw_serran/"
OUTPREFIX="serran_mitoz"
$MITOZ all --create_config
## extractfq
nohup bash extractfq.sh $RAWFQGZ1 $RAWFQGZ2 $FOLDERRAW &
## mitoz
nohup bash mitoz_all.sh $FOLDERRAW $OUTPREFIX &
##extract 5 Go
mkdir 02-raw
$EXTRACT_FQ_SEQ -fq1 $RAWFQGZ1 -fq2 $RAWFQGZ2 -outfq1 02-raw/raw.1.fq -outfq2 02-raw/raw.2.fq -size_required 5
$MITOZ all --genetic_code 2 --clade Chordata --outprefix mito_mullus \
--thread_number 8 \
--fastq1 02-raw/raw.1.fq \
--fastq2 02-raw/raw.2.fq \
--fastq_read_length 150 \
--insert_size 250 \
--run_mode 2 \
--filter_taxa_method 1 \
--requiring_taxa 'Chordata'
/media/bigvol/peguerin
\ No newline at end of file
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