The following shell script was used to run checkM on the 224 C. scindens genomes:
/storage1/data19/Gut_Microbiome_Clostridium_scindens/run_checkm_all_c_scindens_genomes.sh
The exact command that was run using this script was:
checkm lineage_wf Clostridium_scindens_genomes_final/ Clostridium_scindens_genomes_final_checkM -f Clostridium_scindens_genomes_final_checkM_data/ --tab_table --tmpdir tmp_checkm_folder/ -t 10 --pplacer_threads 10 -x fasta
The following shell script was used to run checkM on the 224 C. scindens genomes:
/storage1/data19/Gut_Microbiome_Clostridium_scindens/run_checkm_all_c_scindens_genomes.shThe exact command that was run using this script was:
checkm lineage_wf Clostridium_scindens_genomes_final/ Clostridium_scindens_genomes_final_checkM -f Clostridium_scindens_genomes_final_checkM_data/ --tab_table --tmpdir tmp_checkm_folder/ -t 10 --pplacer_threads 10 -x fasta