{"id":856,"date":"2022-06-23T23:15:47","date_gmt":"2022-06-23T15:15:47","guid":{"rendered":"http:\/\/www.wuchangsong.com\/?p=856"},"modified":"2022-06-23T23:36:45","modified_gmt":"2022-06-23T15:36:45","slug":"checkm%e5%ae%89%e8%a3%85%e5%8f%8a%e4%bd%bf%e7%94%a8","status":"publish","type":"post","link":"http:\/\/www.wuchangsong.com\/?p=856","title":{"rendered":"CheckM\u5b89\u88c5\u53ca\u4f7f\u7528"},"content":{"rendered":"<p>CheckM\u53ef\u4ee5\u7528\u4e8e\u8bc4\u4f30\u5df2\u7ec4\u88c5\u7684\u57fa\u56e0\u7ec4\u6216\u8005\u5b8f\u57fa\u56e0\u7ec4\u5e8f\u5217\u7684\u8d28\u91cf\uff0c\u5305\u62ec\u57fa\u56e0\u7ec4\u5b8c\u6574\u5ea6\u3001\u6c61\u67d3\u5ea6\u3001\u5e8f\u5217\u5206\u5e03\u7b49\u4fe1\u606f\u3002<\/p>\n<pre>##\u901a\u8fc7conda\u5b89\u88c5\nconda create -n checkm\nconda activate checkm\nconda install -c bioconda checkm-genome\n##OR\npip3 install numpy\npip3 install matplotlib\npip3 install pysam\npip3 install checkm-genome\nconda install hmmer prodigal pplacer\n##\u4e0b\u8f7d\u6570\u636e\u5e93\u5e76\u8bbe\u7f6e\u6570\u636e\u8def\u5f84\nwget -c https:\/\/data.ace.uq.edu.au\/public\/CheckM_databases\/checkm_data_2015_01_16.tar.gz\ntar -zxvf checkm_data_2015_01_16.tar.gz\ncheckm data setRoot \/path\/to\/checkm_data\ncheckm lineage_wf -t 150 -x fasta -f sag_2554.txt --tab_table ..\/fasta_file output\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>CheckM\u53ef\u4ee5\u7528\u4e8e\u8bc4\u4f30\u5df2\u7ec4\u88c5\u7684\u57fa\u56e0\u7ec4\u6216\u8005\u5b8f\u57fa\u56e0\u7ec4\u5e8f\u5217\u7684\u8d28\u91cf\uff0c\u5305\u62ec\u57fa\u56e0\u7ec4\u5b8c\u6574\u5ea6\u3001\u6c61\u67d3\u5ea6\u3001\u5e8f\u5217\u5206\u5e03\u7b49\u4fe1\u606f\u3002 ##\u901a\u8fc7conda\u5b89\u88c5 conda create -n checkm conda activate checkm conda install -c bioconda checkm-genome ##OR pip3 install numpy pip3 install matplotlib pip3 install pysam pip3 install checkm-genome conda install hmmer prodigal pplacer ##\u4e0b\u8f7d\u6570\u636e\u5e93\u5e76\u8bbe\u7f6e\u6570\u636e\u8def\u5f84 wget -c https:\/\/data.ace.uq.edu.au\/public\/CheckM_databases\/checkm_data_2015_01_16.tar.gz tar -zxvf checkm_data_2015_01_16.tar.gz checkm data setRoot \/path\/to\/checkm_data checkm lineage_wf -t 150 -x fasta -f sag_2554.txt &#8211;tab_table ..\/fasta_file output<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4],"tags":[],"_links":{"self":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/856"}],"collection":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=856"}],"version-history":[{"count":3,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/856\/revisions"}],"predecessor-version":[{"id":859,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/856\/revisions\/859"}],"wp:attachment":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=856"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=856"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=856"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}