Checkm安装使用教程

安装checkm

安装链接

刚开始用官网命令 conda install hmmer prodigal pplacer 报错

(vicent) yanziming@server1:~/vicent$ conda install hmmer prodigal pplacer
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.PackagesNotFoundError: The following packages are not available from current channels:- prodigal- hmmer- pplacerCurrent channels:- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/linux-64- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/noarch- https://repo.anaconda.com/pkgs/main/linux-64- https://repo.anaconda.com/pkgs/main/noarch- https://repo.anaconda.com/pkgs/r/linux-64- https://repo.anaconda.com/pkgs/r/noarchTo search for alternate channels that may provide the conda package you're
looking for, navigate tohttps://anaconda.organd use the search bar at the top of the page.

去官网搜对应的包，选择对应的版本，找到对应的命令，如下图；

# 安装依赖
conda install -c bioconda prodigal
conda install -c bioconda pplacer
conda install -c bioconda hmmer
# 安装
pip3 install checkm-genome
# 测试
(vicent) yanziming@server1:~/vicent$ checkm
It seems that the CheckM data folder has not been set yet or has been removed. Please run 'checkm data setRoot'.Path [/home/yanziming/.checkm] does not exist so I will attempt to create it
Path [/home/yanziming/.checkm] has been created and you have permission to write to this folder.
(re) creating manifest file (please be patient)....::: CheckM v1.2.2 :::...Lineage-specific marker set:tree         -> Place bins in the reference genome treetree_qa      -> Assess phylogenetic markers found in each binlineage_set  -> Infer lineage-specific marker sets for each binTaxonomic-specific marker set:taxon_list   -> List available taxonomic-specific marker setstaxon_set    -> Generate taxonomic-specific marker setApply marker set to genome bins:analyze      -> Identify marker genes in binsqa           -> Assess bins for contamination and completenessCommon workflows (combines above commands):lineage_wf   -> Runs tree, lineage_set, analyze, qataxonomy_wf  -> Runs taxon_set, analyze, qaReference distribution plots:gc_plot      -> Create GC histogram and delta-GC plotcoding_plot  -> Create coding density (CD) histogram and delta-CD plottetra_plot   -> Create tetranucleotide distance (TD) histogram and delta-TD plotdist_plot    -> Create image with GC, CD, and TD distribution plots togetherGeneral plots:nx_plot      -> Create Nx-plotslen_hist     -> Sequence length histogrammarker_plot  -> Plot position of marker genes on sequencesgc_bias_plot -> Plot bin coverage as a function of GCBin exploration and modification:unique       -> Ensure no sequences are assigned to multiple binsmerge        -> Identify bins with complementary sets of marker genesoutliers     -> [Experimental] Identify outlier in bins relative to reference distributionsmodify       -> [Experimental] Modify sequences in a binUtility functions:unbinned     -> Identify unbinned sequencescoverage     -> Calculate coverage of sequencestetra        -> Calculate tetranucleotide signature of sequencesprofile      -> Calculate percentage of reads mapped to each binssu_finder   -> Identify SSU (16S/18S) rRNAs in sequencesUse 'checkm data setRoot <checkm_data_dir>' to specify the location of CheckM database files.Usage: checkm <command> -h for command specific help

数据下载

数据要不下载之后运行会报文件找不到的错误

链接

# 下载后解压
tar -zxvf checkm_data_2015_01_16.tar.gz

# 运行checkm
checkm lineage_wf -x fasta ./result/ ./result_CHECKM/ -t 30 --tab_table -f test.tab -t 50

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Checkm安装使用教程

安装checkm

数据下载

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