A shell script located at /storage1/data19/Gut_Microbiome_Clostridium_scindens/run_gtdbtk_tamburini.sh was used to run GTDB-Tk on the 1300 genomes from the Tamburini dataset.
The actual command used to run GTDB-Tk on the genomes was:
gtdbtk classify_wf -x fna --cpus 20 --pplacer_cpus 20 --tmpdir gtdbtk_temp_files/ --out_dir GTDBTK_Output_Files_Tamburini_et_al_2021/ --genome_dir Tamburini_et_al_2021/
A shell script located at
/storage1/data19/Gut_Microbiome_Clostridium_scindens/run_gtdbtk_tamburini.shwas used to run GTDB-Tk on the 1300 genomes from the Tamburini dataset.The actual command used to run GTDB-Tk on the genomes was:
gtdbtk classify_wf -x fna --cpus 20 --pplacer_cpus 20 --tmpdir gtdbtk_temp_files/ --out_dir GTDBTK_Output_Files_Tamburini_et_al_2021/ --genome_dir Tamburini_et_al_2021/