metaphlan实际能够使用方法（超详细）

MetaPhlAn2
参考：https://blog.youkuaiyun.com/woodcorpse/article/details/106554425
介绍

用上述的方法进行安装失败：


改用conda去进行安装：
先安装conda


一直按enter，可以看到许可证说明等

接受输入yes，enter

进入minconda3的bin文件夹：
/home/lijing/miniconda3/bin

[lijing@master bin]$ chmod 777 activate
[lijing@master bin]$ …/activate
-bash: …/activate: 没有那个文件或目录
[lijing@master bin]$ . ./activate
(base) [lijing@master bin]$ conda list

退出conda环境和进入conda环境：
[lijing@master bin]$ conda deactivate
[lijing@master bin]$ conda activate

添加频道，官方channel：

创建python2的环境但失败了：
$ conda env list
(base) [lijing@master ~]$ conda create -n python2 python=2

安装参考：https://zouhua.top/archives/9d8099c8.html

安装metaphlan3.0，使用conda进行安装：
conda create --name mpa -c bioconda python=3.7 metaphlan -y

出现问题：
CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/bioconda/linux-64/perl-json-x s-2.34-pl526h6bb024c_3.tar.bz2>
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/bioconda/linux-64/mafft-7.487 -h779adbc_0.tar.bz2>
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

解决错误：

1. (base) [lijing@master metaphlan2]$ conda config --set ssl_verify false
   (base) [lijing@master metaphlan2]$ conda create --name mpa -c bioconda python=3.7 metaphlan -y
   

2.换源：
(base) [lijing@master metaphlan2]$ conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
(base) [lijing@master metaphlan2]$ conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
(base) [lijing@master metaphlan2]$ conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
(base) [lijing@master metaphlan2]$ conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/
(base) [lijing@master metaphlan2]$ conda config --set show_channel_urls yes
(base) [lijing@master metaphlan2]$ conda config --get channels

(base) [lijing@master metaphlan2]$ conda info

找到/home/lijing/.condarc，并打开修改
(base) [lijing@master ~]$ vi .condarc 改为下面的形式，参考：https://blog.youkuaiyun.com/qq_33757398/article/details/105243889

重新下载并完成

(base) [lijing@master ~]$ conda create --name mpa -c bioconda python=3.7 metaphlan -y


出现问题：
(base) [lijing@master ~]$ conda activate mpa
(mpa) [lijing@master ~]$ metaphlan
(mpa) [lijing@master ~]$ metaphlan --install --index mpa_v30_CHOCOPhlAn_201901 --bowtie2db /home/lijing/miniconda3/envs/mpa/lib/python3.7/site-packages/metaphlan/metaphlan_databases

重试还是出问题：
(mpa) [lijing@master bowtie2db]$ metaphlan --install --index mpa_v30_CHOCOPhlAn_201901 --bowtie2db /home/lijing/lijing202110/metaphlan2/bowtie2db
或
(mpa) [lijing@master bowtie2db]$ metaphlan /home/lijing/lijing202110/20211019test-data/NY_test.fq --input_type fastq -o /home/lijing/lijing202110/20211019test-data/ny_metaphlan_out.txt

暂时参考：
https://forum.biobakery.org/t/issue-with-bowtie2db-trying-to-install-metaphian3/1760/2

参考官网：
https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-3.0#installation

继续用另一种方法：
https://blog.youkuaiyun.com/weixin_42072765/article/details/108240712

humann3的安装与使用：解决metaphlan3无法下载数据库的问题。
https://blog.youkuaiyun.com/zhangjunya/article/details/108375691?spm=1001.2101.3001.6650.4&utm_medium=distribute.pc_relevant.none-task-blog-2%7Edefault%7ECTRLIST%7Edefault-4.no_search_link&depth_1-utm_source=distribute.pc_relevant.none-task-blog-2%7Edefault%7ECTRLIST%7Edefault-4.no_search_link