我正在尝试从 https://github.com/YuSugihara/MutMap.git 合并 MutMap 后运行它。起初，我收到错误“bwa not find”，因此我从“https://github.com/lh3/bwa.git”克隆并安装了“bwa”，并将其安装在克隆和安装 MutMap 的本地文件夹中。现在通过运行 mutmap，它给了我同样的错误：
(base) tpl@z4-HP-Z4-G4-WORKSTATION:~/mutmap-git/MutMap/mutmap$ pip install bwa
Requirement already satisfied: bwa in /home/tpl/anaconda3/lib/python3.9/site-packages (1.1.1)
Requirement already satisfied: yagmail>=0.11.214 in /home/tpl/anaconda3/lib/python3.9/site-packages (from bwa) (0.15.293)
Requirement already satisfied: python-telegram-bot in /home/tpl/anaconda3/lib/python3.9/site-packages (from bwa) (20.5)
Requirement already satisfied: requests in /home/tpl/anaconda3/lib/python3.9/site-packages (from bwa) (2.28.1)
Requirement already satisfied: premailer in /home/tpl/anaconda3/lib/python3.9/site-packages (from yagmail>=0.11.214->bwa) (3.10.0)
Requirement already satisfied: httpx~=0.24.1 in /home/tpl/anaconda3/lib/python3.9/site-packages (from python-telegram-bot->bwa) (0.24.1)
Requirement already satisfied: idna<4,>=2.5 in /home/tpl/anaconda3/lib/python3.9/site-packages (from requests->bwa) (3.3)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/tpl/anaconda3/lib/python3.9/site-packages (from requests->bwa) (1.26.11)
Requirement already satisfied: charset-normalizer<3,>=2 in /home/tpl/anaconda3/lib/python3.9/site-packages (from requests->bwa) (2.0.4)
Requirement already satisfied: certifi>=2017.4.17 in /home/tpl/anaconda3/lib/python3.9/site-packages (from requests->bwa) (2023.5.7)
Requirement already satisfied: sniffio in /home/tpl/anaconda3/lib/python3.9/site-packages (from httpx~=0.24.1->python-telegram-bot->bwa) (1.2.0)
Requirement already satisfied: httpcore<0.18.0,>=0.15.0 in /home/tpl/anaconda3/lib/python3.9/site-packages (from httpx~=0.24.1->python-telegram-bot->bwa) (0.17.3)
Requirement already satisfied: cachetools in /home/tpl/anaconda3/lib/python3.9/site-packages (from premailer->yagmail>=0.11.214->bwa) (5.3.1)
Requirement already satisfied: cssutils in /home/tpl/anaconda3/lib/python3.9/site-packages (from premailer->yagmail>=0.11.214->bwa) (2.7.1)
Requirement already satisfied: cssselect in /home/tpl/anaconda3/lib/python3.9/site-packages (from premailer->yagmail>=0.11.214->bwa) (1.1.0)
Requirement already satisfied: lxml in /home/tpl/anaconda3/lib/python3.9/site-packages (from premailer->yagmail>=0.11.214->bwa) (4.9.1)
Requirement already satisfied: anyio<5.0,>=3.0 in /home/tpl/anaconda3/lib/python3.9/site-packages (from httpcore<0.18.0,>=0.15.0->httpx~=0.24.1->python-telegram-bot->bwa) (3.5.0)
Requirement already satisfied: h11<0.15,>=0.13 in /home/tpl/anaconda3/lib/python3.9/site-packages (from httpcore<0.18.0,>=0.15.0->httpx~=0.24.1->python-telegram-bot->bwa) (0.14.0)
(base) tpl@z4-HP-Z4-G4-WORKSTATION:~/mutmap-git/MutMap/mutmap$ mutmap -reference_fasta.fasta -c bam_of_Sp-R.bam -b bam_of_f2R.bam -n 50 -o output1
[MutMap:2023-09-25 13:25:24] start to run MutMap.
[MutMap:2023-09-25 13:25:24] maximum number of threads which you can use is up to 8.
[MutMap:2023-09-25 13:25:24] start to index reference fasta.
[MutMap:2023-09-25 13:25:24] !!ERROR!! bwa index output1/10_ref/eference_fasta.fasta >> output1/log/bwa.log 2>&1
please check below:
/bin/sh: 1: bwa: not found
这个错误是什么以及解决方案是什么？ 预先感谢
收到错误“找不到 bwa”后，我已经从 github 安装了 bwa，但错误仍然存在。
aligner bwa 不是 python 包，因此无法通过 pip 安装它。 python 包 bwa （您安装的）是某种通知发送器，但不是您需要的。您可以通过 conda 安装 bwa，也可以从 GitHub 克隆并编译。只要它在 PATH 中就没有关系。