安装BUSCO和简单使用

作者: 小明的数据分析笔记本 | 来源:发表于2023-04-14 09:58 被阅读0次

BUSCO多样本作图
quast
Docker Busco V4使用过程2020-09-14
Conda BUSCO4的安装以及使用_Augustus物种20
【2021-12-18更新】使用busco时遇到的几个bug的修
busco 3.0.2安装
Conda 安装 Busco
busco软件使用详解
BUSCO 安装备忘
CocoaPods 的安装和使用介绍

BUSCO的主页

https://busco.ezlab.org/

直接选择conda安装了

conda create -n busco5.4.6
conda activate busco5.4.6
conda install busco=5.4.6 -y

报了很多错

Preparing transaction: done                                                                                                                                                         
Verifying transaction: |                                                                                                                                                            
SafetyError: The package for r-base located at /home/myan/anaconda3/pkgs/r-base-4.2.2-h6b4767f_2                                                                                    
appears to be corrupted. The path 'lib/R/doc/html/packages.html'                                                                                                                    
has an incorrect size.                                                                                                                                                              
  reported size: 3423 bytes                                                                                                                                                         
  actual size: 10803 bytes                                                                                                                                                          
                                                                                                                                                                                    
ClobberError: This transaction has incompatible packages due to a shared path.                                                                                                      
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::entrez-direct-16.2-he881be0_1, https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::bbmap-39.01-h5c4e2a8_0                                                                                                                                                                             
  path: 'bin/build_env_setup.sh'                                                                                                                                                    
                                                                                                                                                                                    
                                                                                                                                                                                    
ClobberError: This transaction has incompatible packages due to a shared path.                                                                                                      
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::entrez-direct-16.2-he881be0_1, https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::bbmap-39.01-h5c4e2a8_0                                                                                                                                                                             
  path: 'bin/conda_build.sh'                                                                                                                                                        
                                                                                                                                                                                    
                                                                                                                                                                                    
ClobberError: This transaction has incompatible packages due to a shared path.                                                                                                      
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-params-util-1.102-pl5321h9f5acd7_1, https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-package-stash-0.40-pl5321h87f3376_1                                                                                                                                                 
  path: 'lib/perl5/5.32/site_perl/Params/Util.pm'                                                                                                                                   
                                                                                                                                                                                    
                                                                                                                                                                                    
ClobberError: This transaction has incompatible packages due to a shared path.                                                                                                      
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-params-util-1.102-pl5321h9f5acd7_1, https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-package-stash-0.40-pl5321h87f3376_1                                                                                                                                                 
  path: 'lib/perl5/5.32/site_perl/Params/Util/PP.pm'                                                                                                                                
                                                                                                                                                                                    
                                                                                                                                                                                    
ClobberError: This transaction has incompatible packages due to a shared path.                                                                                                      
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-params-util-1.102-pl5321h9f5acd7_1, https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-package-stash-0.40-pl5321h87f3376_1                                                                                                                                                 
  path: 'lib/perl5/5.32/site_perl/auto/Params/Util/.packlist'                                                                                                                       
                      

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-params-util-1.102-pl5321h9f5acd7_1, https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-package-stash-0.40-pl5321h87f3376_1
  path: 'lib/perl5/5.32/site_perl/auto/Params/Util/Util.so'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-params-util-1.102-pl5321h9f5acd7_1, https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-package-stash-0.40-pl5321h87f3376_1
  path: 'man/man3/Params::Util.3'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-params-util-1.102-pl5321h9f5acd7_1, https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-package-stash-0.40-pl5321h87f3376_1
  path: 'man/man3/Params::Util::PP.3'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/noarch::perl-sub-install-0.928-pl5321hdfd78af_3, https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-package-stash-0.40-pl5321h87f3376_1
  path: 'lib/perl5/5.32/site_perl/auto/Sub/Install/.packlist'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/noarch::perl-sub-install-0.928-pl5321hdfd78af_3, https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-package-stash-0.40-pl5321h87f3376_1
  path: 'lib/perl5/site_perl/Sub/Install.pm'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/noarch::perl-sub-install-0.928-pl5321hdfd78af_3, https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-package-stash-0.40-pl5321h87f3376_1
  path: 'man/man3/Sub::Install.3'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/noarch::perl-data-optlist-0.112-pl5321hdfd78af_0, https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-package-stash-0.40-pl5321h87f3376_1
  path: 'lib/perl5/5.32/site_perl/auto/Data/OptList/.packlist'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/noarch::perl-data-optlist-0.112-pl5321hdfd78af_0, https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-package-stash-0.40-pl5321h87f3376_1
  path: 'lib/perl5/site_perl/Data/OptList.pm'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/noarch::perl-data-optlist-0.112-pl5321hdfd78af_0, https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-package-stash-0.40-pl5321h87f3376_1
  path: 'man/man3/Data::OptList.3'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-package-stash-0.40-pl5321h87f3376_1, https://mirrors.aliyun.com/anaconda/cloud/bioconda/noarch::perl-sub-exporter-0.988-pl5321hdfd78af_0
  path: 'lib/perl5/5.32/site_perl/auto/Sub/Exporter/.packlist'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-package-stash-0.40-pl5321h87f3376_1, https://mirrors.aliyun.com/anaconda/cloud/bioconda/noarch::perl-sub-exporter-0.988-pl5321hdfd78af_0
  path: 'lib/perl5/site_perl/Sub/Exporter.pm'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-package-stash-0.40-pl5321h87f3376_1, https://mirrors.aliyun.com/anaconda/cloud/bioconda/noarch::perl-sub-exporter-0.988-pl5321hdfd78af_0
  path: 'lib/perl5/site_perl/Sub/Exporter/Cookbook.pod'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-package-stash-0.40-pl5321h87f3376_1, https://mirrors.aliyun.com/anaconda/cloud/bioconda/noarch::perl-sub-exporter-0.988-pl5321hdfd78af_0
  path: 'lib/perl5/site_perl/Sub/Exporter/Tutorial.pod'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-package-stash-0.40-pl5321h87f3376_1, https://mirrors.aliyun.com/anaconda/cloud/bioconda/noarch::perl-sub-exporter-0.988-pl5321hdfd78af_0
  path: 'lib/perl5/site_perl/Sub/Exporter/Util.pm'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-package-stash-0.40-pl5321h87f3376_1, https://mirrors.aliyun.com/anaconda/cloud/bioconda/noarch::perl-sub-exporter-0.988-pl5321hdfd78af_0
  path: 'man/man3/Sub::Exporter.3'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-package-stash-0.40-pl5321h87f3376_1, https://mirrors.aliyun.com/anaconda/cloud/bioconda/noarch::perl-sub-exporter-0.988-pl5321hdfd78af_0
  path: 'man/man3/Sub::Exporter::Cookbook.3'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-package-stash-0.40-pl5321h87f3376_1, https://mirrors.aliyun.com/anaconda/cloud/bioconda/noarch::perl-sub-exporter-0.988-pl5321hdfd78af_0
  path: 'man/man3/Sub::Exporter::Tutorial.3'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: https://mirrors.aliyun.com/anaconda/cloud/bioconda/linux-64::perl-package-stash-0.40-pl5321h87f3376_1, https://mirrors.aliyun.com/anaconda/cloud/bioconda/noarch::perl-sub-exporter-0.988-pl5321hdfd78af_0
  path: 'man/man3/Sub::Exporter::Util.3'


                                                                                                                                                                                  done
Executing transaction: done

暂时不清楚是什么原因，不过好像不影响使用

下载植物的库

下载链接

https://busco-data.ezlab.org/v5/data/lineages/

https://busco-data.ezlab.org/v5/data/lineages/eukaryota_odb10.2020-09-10.tar.gz

tar -xzvf eukaryota_odb10.2020-09-10.tar.gz

用拟南芥的数据试试

busco -i ../ref.fa -l /home/myan/my_data/database/eukaryota_odb10/ -o at -m genome --force --offline --augustus --cpu 8

6分钟就运行完了

at/short_summary.specific.eukaryota_odb10.at.txt 有后续用于画图的内容

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