First version guppy_tombo_deepsignal_plant

Scripts/sbatch_deepsignalplant.sh

+#!/bin/bash
+​
+### BY EL KHADDAR FADWA 
+​
+#SBATCH -J DeepSignal_Plant
+
+#SBATCH --mail-user fadwael.khaddar@ird.fr
+#SBATCH --mail-type=ALL
+​
+#SBATCH -e DeepSignal_Plant."%j".err
+#SBATCH -o DeepSignal_Plant."%j".out
+​
+#SBATCH -p gpu
+#SBATCH -A gpu_group
+#SBATCH -c 8
+#SBATCH --gres=gpu:4
+
+
+# Loading module
+
+
+module load system/Miniconda2/4.3.31
+module load system/cuda/11.4
+module load bioinfo/tombo/1.5.1
+module load bioinfo/guppy-gpu/6.3.7
+
+# Arguments 
+
+yml_file=$1
+INPUT=$2
+OUTPUT=$3
+NAME=$4
+REF=$5
+MODEL=$6
+
+# RUNNING GUPPY 
+
+echo " BASECALLING USING GUPPY "
+
+# Paramètre d'utilisation guppy 
+
+guppy_conf="dna_r9.4.1_450bps_hac_prom.cfg"
+
+
+
+#	1. Basecalling
+
+guppy_basecaller -i ${INPUT} -r -s ${OUTPUT} \
+  --config $guppy_conf \
+  --device CUDA:0
+
+# 	2. Concatenation of fastq
+
+cd ${OUTPUT}/pass/ 
+
+cat *.fastq > ${NAME}_Guppy.fastq
+
+# RUNNING TOMBO
+
+# Paramètre d'utilisation TOMBO
+
+basecall_group="Basecall_1D_000"
+basecall_subgroupe="BaseCalled_template"
+corrected_group="RawGenomeCorrected_000"
+
+
+echo " RUNNING TOMBO "
+
+cd 
+
+cd ${INPUT} 
+
+wget https://github.com/nanoporetech/vbz_compression/releases/download/v1.0.1/ont-vbz-hdf-plugin-1.0.1-Linux-x86_64.tar.gz
+
+tar zxvf ont-vbz-hdf-plugin-1.0.1-Linux-x86_64.tar.gz
+
+export HDF5_PLUGIN_PATH=ont-vbz-hdf-plugin-1.0.1-Linux/usr/local/hdf5/lib/plugin/
+
+#	1. Tombo preprocess 
+
+
+tombo preprocess annotate_raw_with_fastqs --fast5-basedir ${INPUT}   --fastq-filenames ${OUTPUT}/pass/${NAME}_Guppy.fastq  --sequencing-summary-filenames ${OUTPUT}/sequencing_summary.txt   --basecall-group $basecall_group --basecall-subgroup $basecall_subgroupe --overwrite --processes 10
+
+
+
+#	2. Tombo resquiggle 
+
+
+tombo resquiggle ${INPUT} ${REF}  --processes 10 --corrected-group $corrected_group   --basecall-group $basecall_group --overwrite
+
+### RUNNING DEEPSIGNAL_PLANT 
+
+echo " RUNNING DEEPSIGNAL-PLANT " 
+
+# Conda environement creation
+
+conda create env -f $yml_file 
+
+source activate deepsignalpenv
+
+
+# Paramètre d'utilisation de DeepSignal_Plant 
+
+nproc=20
+ngpu=4
+
+#	1. Call modifications
+
+CUDA_VISIBLE_DEVICES=0 deepsignal_plant call_mods --input_path ${INPUT}  --model_path ${MODEL}   --result_file  ${OUTPUT}/${NAME}_call_mods.tsv --corrected_group $corrected_group --motifs C --nproc $nproc --nproc_gpu $ngpu
+
+
+#	2. Call mod frequency: tsv 
+
+deepsignal_plant call_freq --input_path ${OUTPUT}/${NAME}_call_mods.tsv --result_file ${OUTPUT}/${NAME}_call_mods.frequency.tsv
+
+
+# 	3. Call mod frenquency: bed
+
+deepsignal_plant call_freq --input_path ${OUTPUT}/${NAME}_call_mods.tsv --result_file ${OUTPUT}/${NAME}_call_mods.frequency.bed --bed --sort 
+
+
+
+
+
+
+
+
+
+​