Run GTDB-Tk on the 32,000 Zeng genomes - Githubissues

breister2 / Clostridium_scindens_mining

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Run GTDB-Tk on the 32,000 Zeng genomes #5

Open breister2 opened 1 year ago

breister2 commented 1 year ago

GTDB-Tk was run using the following shell script: /storage1/data19/Gut_Microbiome_Clostridium_scindens/run_gtdbtk_Zeng.sh

The exact GTDB-Tk command that was run was: gtdbtk classify_wf -x gz --cpus 20 --pplacer_cpus 20 --tmpdir gtdbtk_temp_files/ --out_dir GTDBTK_Output_Files_Zeng_et_al_2022/ --genome_dir Zeng_et_al_2022/

breister2 commented 1 year ago

The resulting GTDB-Tk output identified the following genomes as C. scindens:

BackhedF_2015_ERR525896_bin.18.fna
BackhedF_2015_ERR525961_bin.14.fna
BackhedF_2015_ERR525992_bin.38.fna
BackhedF_2015_ERR526080_bin.17.fna
Baumann-DudenhoefferAM_2018_SRR7217830_bin.1.fna
CasaburiG_2019_SRR6277114_bin.5.fna
CokerMO_2019_SRR8692178_bin.1.fna
CokerMO_2019_SRR8692181_bin.17.fna
CokerMO_2019_SRR8692192_bin.27.fna
CokerMO_2019_SRR8692210_bin.15.fna
MurphyR_2019_SRR7351692_bin.11.fna
MurphyR_2019_SRR7351790_bin.1.fna
MurphyR_2019_SRR7351869_bin.8.fna
MurphyR_2019_SRR7352056_bin.5.fna
MurphyR_2019_SRR7411324_bin.13.fna
ParnanenK_2018_SRR5723857_bin.3.fna