文献 1
标题：A complete domain-to-species taxonomy for Bacteria and Archaea
中文：细菌古菌注释到种
杂志：NBT
时间：2020
摘要：
基因组分类学数据库是一种系统发育一致的、基于基因组的分类学，提供了约15万个细菌和古细菌基因组从域到属的有序分类。然而，基因组分类数据库中几乎40%的基因组没有物种名。我们通过使用普遍接受的平均核苷酸鉴定标准来设定物种界限，并提出包含所有公开可用的细菌和古细菌基因组的物种群，来解决这一限制。与以往一般的核苷酸鉴定研究不同，我们选择了一个具有代表性的基因组作为定义每个物种的有效命名“类型”。在24706个提议的物种群中，8792个是基于已发表的名称。我们为剩余的15914个物种cluster指定了占位符名称，为越来越多的未栽培物种的基因组提供名称。该资源为细菌和古细菌基因组提供了一个完整的从域到种的分类框架，这将有助于对未栽培物种的研究和提高科学结果的交流。
GTDB Species Cluster Toolkit:
https://github.com/Ecogenomics/gtdb-species-clusters
文献2：
标题：GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
中文：用GTDB数据库注释基因组的工具
杂志：Bioinformatics
时间：2019
GTDB-Tk：https://github.com/ecogenomics/gtdbtk
Bioconda: https://ecogenomics.github.io/GTDBTk/installing/bioconda.html
官网：https://gtdb.ecogenomic.org/
新版安装
# 最新版
conda create -n gtdbtk-2.3.2 -c conda-forge -c bioconda gtdbtk=2.3.2
conda activate gtdbtk-2.3.2
# 配置数据库
conda env config vars set GTDBTK_DATA_PATH="/hwfsxx1/ST_HN/P18Z10200N0423/huty/databases/GTDB_214.1/release214/"
# 检测
gtdbtk check_install
[2023-08-31 16:01:13] INFO: GTDB-Tk v2.3.2
[2023-08-31 16:01:13] INFO: gtdbtk check_install
[2023-08-31 16:01:13] INFO: Using GTDB-Tk reference data version r214: /hwfsxx1/ST_HN/P18Z10200N0423/huty/databases/GTDB_214.1/release214
[2023-08-31 16:01:13] INFO: Running install verification
[2023-08-31 16:01:13] INFO: Checking that all third-party software are on the system path:
[2023-08-31 16:01:13] INFO: |-- FastTree OK
[2023-08-31 16:01:13] INFO: |-- FastTreeMP OK
[2023-08-31 16:01:13] INFO: |-- fastANI OK
[2023-08-31 16:01:13] INFO: |-- guppy OK
[2023-08-31 16:01:13] INFO: |-- hmmalign OK
[2023-08-31 16:01:13] INFO: |-- hmmsearch OK
[2023-08-31 16:01:13] INFO: |-- mash OK
[2023-08-31 16:01:13] INFO: |-- pplacer OK
[2023-08-31 16:01:13] INFO: |-- prodigal OK
[2023-08-31 16:01:13] INFO: Checking integrity of reference package: /hwfsxx1/ST_HN/P18Z10200N0423/huty/databases/GTDB_214.1/release214
[2023-08-31 16:01:15] INFO: |-- pplacer OK
[2023-08-31 16:01:15] INFO: |-- masks OK
[2023-08-31 16:01:24] INFO: |-- markers OK %)
[2023-08-31 16:01:24] INFO: |-- radii OK
[2023-08-31 16:01:35] INFO: |-- msa OK
[2023-08-31 16:01:35] INFO: |-- metadata OK
[2023-08-31 16:01:35] INFO: |-- taxonomy OK
历史版本
1 conda安装
# latest version
conda create -n gtdbtk -c conda-forge -c bioconda
conda activate gtdbtk
conda install -c conda-forge -c bioconda gtdbtk
gtdbtk版本
gtdbtk --help
...::: GTDB-Tk v1.0.2 :::...
指定版本安装
conda install -c conda-forge -c bioconda gtdbtk=2.1.0
#conda install -c conda-forge -c bioconda gtdbtk=2.1.1
gtdbtk -h
2 数据库
版本
下载数据库
nohup wget -c https://data.ace.uq.edu.au/public/gtdb/data/releases/release207/207.0/auxillary_files/gtdbtk_r207_v2_data.tar.gz &
# 数据库太大了，找专业人士帮忙下载
tar -zxvf gtdbtk_r207_v2_data.tar.gz
ls
# gtdbtk_r207_v2_data.tar.gz release207_v2
3 数据库配置
# Determine the GTDB-Tk environment path
conda activate gtdbtk
which gtdbtk
# /miniconda3/envs/gtdbtk/bin/gtdbtk
# 3.1 Edit the activate file
echo "export GTDBTK_DATA_PATH=/path/to/release/package/" > /miniconda3/envs/gtdbtk/etc/conda/activate.d/gtdbtk.sh
# OR 3.2 /miniconda3/envs/gtdbtk/etc/conda/activate.d/不存在，解决办法
conda env config vars set GTDBTK_DATA_PATH="/public/home/zzumgg03/huty/databases/gtdb_v207/release207_v2/"
# To make your changes take effect please reactivate your environment
3 使用方法
gtdbtk --help
gtdbtk classify_wf --help
# 使用方法
usage: gtdbtk classify_wf (--genome_dir GENOME_DIR | --batchfile BATCHFILE)
--out_dir OUT_DIR [-x EXTENSION]
[--min_perc_aa MIN_PERC_AA] [--prefix PREFIX]
[--cpus CPUS] [--force] [--scratch_dir SCRATCH_DIR]
[-r] [-d] [-h]
参数：
classify_wf -> Classify genomes by placement in GTDB reference tree
--cpus CPUS number of CPUs to use (default: 1)
-x, --extension EXTENSION extension of files to process, gz = gzipped (default: fna)
--genome_dir GENOME_DIR directory containing genome files in FASTA format
--out_dir OUT_DIR directory to output files
4 注释MAG
gtdbtk classify_wf \
--cpus 16 \
-x fa \
--genome_dir bins_drep_comp70/dereplicated_genomes/ \
--out_dir anno_drep_comp70/
error -> 更新软件到2.1.0
[2022-05-19 09:28:29] INFO: GTDB-Tk v1.0.2
[2022-05-19 09:28:29] INFO: gtdbtk classify_wf --cpus 32 -x fa --genome_dir bins_drep_comp70/dereplicated_genomes/ --out_dir anno_drep_comp70/
[2022-05-19 09:28:29] INFO: Using GTDB-Tk reference data version r207: /hwfssz1/ST_HEALTH/P18Z10200N0423/hutongyuan/databases/release207_v2/
[2022-05-19 09:28:30] INFO: Identifying markers in 120 genomes with 32 threads.
[2022-05-19 09:28:31] INFO: Running Prodigal V2.6.3 to identify genes.
==> Finished processing 120 of 120 (100.0%) genomes.
[2022-05-19 09:35:02] INFO: Identifying TIGRFAM protein families.
==> Finished processing 120 of 120 (100.0%) genomes.
[2022-05-19 09:36:18] INFO: Identifying Pfam protein families.
==> Finished processing 120 of 120 (100.0%) genomes.
[2022-05-19 09:36:24] INFO: Annotations done using HMMER 3.3.2 (Nov 2020)
[2022-05-19 09:36:42] INFO: Done.
[2022-05-19 09:36:43] ERROR: Uncontrolled exit resulting from an unexpected error.
================================================================================
EXCEPTION: FileNotFoundError
MESSAGE: [Errno 2] No such file or directory: '/hwfssz1/ST_HEALTH/P18Z10200N0423/hutongyuan/databases/release207_v2/markers/pfam/individual_hmms/PF00380.14.hmm'
________________________________________________________________________________
5 指定版本安装，配置，使用，结果
# 安装
conda install -c conda-forge -c bioconda gtdbtk=2.1.0
# 配置数据库
echo "export GTDBTK_DATA_PATH=/hwfssz1/ST_HEALTH/P18Z10200N0423/hutongyuan/databases/release207_v2/" > /hwfssz1/ST_HEALTH/P18Z10200N0423/hutongyuan/softwares/miniconda3/envs/gtdbtk/etc/conda/activate.d/gtdbtk.sh
# 参数
source /hwfssz1/ST_HEALTH/P18Z10200N0423/hutongyuan/softwares/miniconda3/etc/profile.d/conda.sh
conda activate gtdbtk
gtdbtk classify_wf \
--cpus 32 \
-x fa \
--genome_dir bins_drep_comp70/dereplicated_genomes/ \
--out_dir anno_drep_comp70/
# 提交任务
qsub -cwd -l vf=200G,p=32 -q st_supermem.q -P st_supermem -binding linear:8 ./sc_gtdb.sh
过程
结果
建树
gtdbtk infer --msa_file align/gtdbtk.bac120.user_msa.fasta.gz \
--out_dir infer_tree --cpus 8
过程
[2022-12-05 11:47:29] INFO: GTDB-Tk v2.1.0
[2022-12-05 11:47:29] INFO: gtdbtk infer --msa_file align/gtdbtk.bac120.user_msa.fasta.gz --out_dir infer_tree --cpus 8
[2022-12-05 11:47:29] INFO: Using GTDB-Tk reference data version r207: /hwfssz1/ST_HEALTH/P18Z10200N0423/hutongyuan/databases/release207_v2/
[2022-12-05 11:47:29] INFO: Inferring FastTree (WAG, SH support values) using a maximum of 8 CPUs.
[2022-12-05 11:48:20] INFO: FastTree version: 2.1.11
[2022-12-05 11:48:20] INFO: Done.
