pwd
/scratch_vol1/fungi

cd -place_in_your_local_computer
git clone https://github.com/PLStenger/Jaunet.git

# For run all pipeline, lunch only this command line : 
time nohup bash 000_run_all_pipeline_in_one_script.sh &> 000_run_all_pipeline_in_one_script.out

time nohup bash 00_quality_check_by_FastQC.sh &> 00_quality_check_by_FastQC.out
>

time nohup bash 01_renamed_sequences.sh &> 01_renamed_sequences.out
>real	0m9,114s
>user	0m0,355s
>sys	0m6,420s

 
time nohup bash 02_trimmomatic_q30.sh &> 02_trimmomatic_q30.out
>real    74m13,168s
>user    535m20,636s
>sys     24m43,419s

time nohup bash 03_cleaned_data_quality_check_by_FastQC.sh &> 03_cleaned_data_quality_check_by_FastQC.out
>real    44m31,850s
>user    69m36,311s
>sys     3m45,328s

time nohup bash 04_qiime2_import_PE.sh &> 04_qiime2_import_PE.out
>real    3m46,676s
>user    3m44,336s
>sys     0m35,434s

time nohup bash 05_qiime2_denoise_PE.sh &> 05_qiime2_denoise_PE.out
>real    103m44,848s
>user    484m44,613s
>sys     10m8,215s

time nohup bash 06_qiime2_tree_PE.sh &> 06_qiime2_tree_PE.out
>real    2m35,519s
>user    2m47,075s
>sys     0m29,329s

time nohup bash 07_qiime2_rarefaction_PE.sh &> 07_qiime2_rarefaction_PE.out
>

time nohup bash 08_qiime2_calculate_and_explore_diversity_metrics_PE.sh &> 08_qiime2_calculate_and_explore_diversity_metrics_PE.out
>real    8m20,030s
>user    15m8,885s
>sys     3m9,577s

time nohup bash 09_core_biom_PE.sh &> 09_core_biom_PE.out
>real    0m38,909s
>user    0m47,948s
>sys     0m17,655s

time nohup bash 10_qiime2_assign_taxonomy_PE.sh &> 10_qiime2_assign_taxonomy_PE.out
>real    315m49,992s
>user    308m4,774s
>sys     7m53,232s