dRep-基因组质控、去冗余及物种界定

Install

(base) [yut@io02 01_Morchella]$ mamba create -n drep -c bioconda drep

依赖关系

dRep 需要其他程序才能运行。并非所有操作都需要所有依赖程序，要检查系统中安装了哪些依赖项，dRep 可以访问这些依赖项，请运行

(drep) [yut@io02 01_Morchella]$ dRep check_dependencies
mash.................................... all good        (location = /datanode02/yut/Software/Miniconda3/envs/drep/bin/mash)
nucmer.................................. all good        (location = /datanode02/yut/Software/Miniconda3/envs/drep/bin/nucmer)
checkm.................................. !!! ERROR !!!   (location = None)
ANIcalculator........................... !!! ERROR !!!   (location = None)
prodigal................................ all good        (location = /datanode02/yut/Software/Miniconda3/envs/drep/bin/prodigal)
centrifuge.............................. !!! ERROR !!!   (location = None)
nsimscan................................ !!! ERROR !!!   (location = None)
fastANI................................. !!! ERROR !!!   (location = /datanode02/yut/Software/Miniconda3/envs/drep/bin/fastANI)

• 安装其他依赖

# install 
$ mamba install -c bioconda checkm-genome

# download database
$ wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
$ [/datanode02/yut/Database/checkm_data_2015_01_16] tar -zxvf checkm_data_2015_01_16.tar.gz
(drep) [yut@node02 checkm_data_2015_01_16]$ checkm data  setRoot /datanode02/yut/Database/checkm_data_2015_01_16
[2023-11-10 20:06:35] INFO: CheckM v1.2.2
[2023-11-10 20:06:35] INFO: checkm data setRoot /datanode02/yut/Database/checkm_data_2015_01_16
[2023-11-10 20:06:35] INFO: CheckM data: /datanode02/yut/.checkm
[2023-11-10 20:06:35] INFO: [CheckM - data] Check for database updates. [setRoot]

Path [/datanode02/yut/Database/checkm_data_2015_01_16] exists and you have permission to write to this folder.
(re) creating manifest file (please be patient).

Path