mitoZ factorized

mitoZ/extractfq.sh

+## 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

mitoZ/mitoz_all.sh

 ## 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 \

mitoZ/script.sh

@@ -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