Pycnandra acuminata https://endemia.nc/flore/fiche1257 Pycnandra fastuosa https://endemia.nc/flore/fiche1253
Click here to see how to install this pipeline
First, open your terminal. Then, run these two command lines :
pwd
/scratch_vol1/fungi
cd -place_in_your_local_computer
git clone https://github.com/PLStenger/Pycnandra.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
>real 15m57,102s
>user 25m7,809s
>sys 1m18,931s
time nohup bash 01_pooling_sequences.sh &> 01_pooling_sequences.out
>real 0m2,227s
>user 0m0,139s
>sys 0m2,081s
time nohup bash 02_trimmomatic_q30.sh &> 02_trimmomatic_q30.out
>real 14m42,465s
>user 112m16,534s
>sys 4m31,750s
time nohup bash 03_cleaned_data_quality_check_by_FastQC.sh &> 03_cleaned_data_quality_check_by_FastQC.out
>real 14m36,768s
>user 22m51,308s
>sys 1m8,843s
time nohup bash 04_qiime2_import_PE.sh &> 04_qiime2_import_PE.out
>real 2m7,230s
>user 2m14,750s
>sys 0m29,133s
time nohup bash 05_qiime2_denoise_PE.sh &> 05_qiime2_denoise_PE.out
>
>
>
time nohup bash 06_qiime2_tree_PE.sh &> 06_qiime2_tree_PE.out
>real 2m22,561s
>user 2m33,893s
>sys 0m31,216s
time nohup bash 07_qiime2_rarefaction_PE.sh &> 07_qiime2_rarefaction_PE.out
>real 1m28,392s
>user 3m26,301s
>sys 0m19,600s
time nohup bash 08_qiime2_calculate_and_explore_diversity_metrics_PE.sh &> 08_qiime2_calculate_and_explore_diversity_metrics_PE.out
>real 10m23,245s
>user 14m32,175s
>sys 2m15,685s
time nohup bash 09_core_biom_PE.sh &> 09_core_biom_PE.out
>real 0m40,582s
>user 0m50,942s
>sys 0m19,471s
time nohup bash 10_qiime2_assign_taxonomy_PE.sh &> 10_qiime2_assign_taxonomy_PE.out
>real 314m58,189s
>user 307m40,973s
>sys 7m31,091s