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run_diann.sh
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#!/bin/bash
#SBATCH -J run_diann
#SBATCH -t 1-00:00:00
#SBATCH -c 32
#SBATCH --mem=110G
#SBATCH --mail-type=END
#SBATCH [email protected]
temp_dir="$HOME"/temp
fasta_file="$HOME"/data/UP000000589_10090.fasta
diann-1.8.1 --f /u/onse/data/2024May_Onur/20240504_OA4_33min_EdRo_SA_ER586_Onur_Input_Experiment_slideB_25_shape_2.mzML --f /u/onse/data/2024May_Onur/20240504_OA4_33min_EdRo_SA_ER586_Onur_Input_Experiment_slideB_1000_shape_1.mzML --f /u/onse/data/2024May_Onur/20240504_OA4_33min_EdRo_SA_ER586_Onur_Input_Experiment_slideB_125_shape_2.mzML --f /u/onse/data/2024May_Onur/20240504_OA4_33min_EdRo_SA_ER586_Onur_Input_Experiment_slideB_250_shape_1.mzML --f /u/onse/data/2024May_Onur/20240504_OA4_33min_EdRo_SA_ER586_Onur_Input_Experiment_slideB_50_shape_1.mzML --f /u/onse/data/2024May_Onur/20240504_OA4_33min_EdRo_SA_ER586_Onur_Input_Experiment_slideB_25_shape_1.mzML --f /u/onse/data/2024May_Onur/20240504_OA4_33min_EdRo_SA_ER586_Onur_Input_Experiment_slideB_50_shape_2.mzML --f /u/onse/data/2024May_Onur/20240504_OA4_33min_EdRo_SA_ER586_Onur_Input_Experiment_slideB_500_shape_1.mzML --f /u/onse/data/2024May_Onur/20240504_OA4_33min_EdRo_SA_ER586_Onur_Input_Experiment_slideB_125_shape_1.mzML --f /u/onse/data/2024May_Onur/20240504_OA4_33min_EdRo_SA_ER586_Onur_Input_Experiment_slideB_500_shape_0.mzML --f /u/onse/data/2024May_Onur/20240504_OA4_33min_EdRo_SA_ER586_Onur_Input_Experiment_slideB_blank_1.mzML --f /u/onse/data/2024May_Onur/20240504_OA4_33min_EdRo_SA_ER586_Onur_Input_Experiment_slideB_blank_0.mzML --f /u/onse/data/2024May_Onur/20240504_OA4_33min_EdRo_SA_ER586_Onur_Input_Experiment_slideB_50_shape_0.mzML --f /u/onse/data/2024May_Onur/20240504_OA4_33min_EdRo_SA_ER586_Onur_Input_Experiment_slideB_blank_2.mzML --f /u/onse/data/2024May_Onur/20240504_OA4_33min_EdRo_SA_ER586_Onur_Input_Experiment_slideB_250_shape_0.mzML --f /u/onse/data/2024May_Onur/20240504_OA4_33min_EdRo_SA_ER586_Onur_Input_Experiment_slideB_250_shape_2.mzML --f /u/onse/data/2024May_Onur/20240504_OA4_33min_EdRo_SA_ER586_Onur_Input_Experiment_slideB_125_shape_0.mzML --f /u/onse/data/2024May_Onur/20240504_OA4_33min_EdRo_SA_ER586_Onur_Input_Experiment_slideB_1000_shape_0.mzML --f /u/onse/data/2024May_Onur/20240504_OA4_33min_EdRo_SA_ER586_Onur_Input_Experiment_slideB_1000_shape_2.mzML --f /u/onse/data/2024May_Onur/20240504_OA4_33min_EdRo_SA_ER586_Onur_Input_Experiment_slideB_500_shape_2.mzML --f /u/onse/data/2024May_Onur/20240504_OA4_33min_EdRo_SA_ER586_Onur_Input_Experiment_slideB_25_shape_0.mzML --lib --threads 64 --verbose 4 --out /u/onse/report.tsv --qvalue 0.01 --matrices --out-lib /u/onse/report-lib.tsv --gen-spec-lib --predictor --fasta /u/onse/data/UP000000589_10090.fasta --fasta-search --min-fr-mz 200 --max-fr-mz 1800 --met-excision --cut K*,R* --missed-cleavages 1 --min-pep-len 6 --max-pep-len 32 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 1 --max-pr-charge 6 --unimod4 --var-mods 1 --double-search --individual-mass-acc --individual-windows --reanalyse --relaxed-prot-inf --smart-profiling --pg-level 1 --peak-center --no-ifs-removal