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
  - pplacer

Current 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/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and 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 tree
    tree_qa      -> Assess phylogenetic markers found in each bin
    lineage_set  -> Infer lineage-specific marker sets for each bin

  Taxonomic-specific marker set:
    taxon_list   -> List available taxonomic-specific marker sets
    taxon_set    -> Generate taxonomic-specific marker set

  Apply marker set to genome bins:
    analyze      -> Identify marker genes in bins
    qa           -> Assess bins for contamination and completeness

  Common workflows (combines above commands):
    lineage_wf   -> Runs tree, lineage_set, analyze, qa
    taxonomy_wf  -> Runs taxon_set, analyze, qa

  Reference distribution plots:
    gc_plot      -> Create GC histogram and delta-GC plot
    coding_plot  -> Create coding density (CD) histogram and delta-CD plot
    tetra_plot   -> Create tetranucleotide distance (TD) histogram and delta-TD plot
    dist_plot    -> Create image with GC, CD, and TD distribution plots together

  General plots:
    nx_plot      -> Create Nx-plots
    len_hist     -> Sequence length histogram
    marker_plot  -> Plot position of marker genes on sequences
    gc_bias_plot -> Plot bin coverage as a function of GC

  Bin exploration and modification:
    unique       -> Ensure no sequences are assigned to multiple bins
    merge        -> Identify bins with complementary sets of marker genes
    outliers     -> [Experimental] Identify outlier in bins relative to reference distributions
    modify       -> [Experimental] Modify sequences in a bin

  Utility functions:
    unbinned     -> Identify unbinned sequences
    coverage     -> Calculate coverage of sequences
    tetra        -> Calculate tetranucleotide signature of sequences
    profile      -> Calculate percentage of reads mapped to each bin
    ssu_finder   -> Identify SSU (16S/18S) rRNAs in sequences

  Use '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