{"id":2618,"date":"2018-09-02T14:21:45","date_gmt":"2018-09-02T06:21:45","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2618"},"modified":"2018-09-04T14:51:48","modified_gmt":"2018-09-04T06:51:48","slug":"%e5%ae%89%e8%a3%85%e9%ab%98%e7%89%88%e6%9c%acsmrt-analysis%e8%bd%af%e4%bb%b6","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2618","title":{"rendered":"\u4f7f\u7528\u9ad8\u7248\u672cSMRT Analysis\u8f6f\u4ef6\u5bf9Pacbio reads\u8fdb\u884c\u57fa\u56e0\u7ec4De novo\u7ec4\u88c5"},"content":{"rendered":"<h1>1. SMRT Analysis\u7b80\u4ecb<\/h1>\n<p>SMRT Analysis\u8f6f\u4ef6\u662f\u7531Pacbio Science\u516c\u53f8\u5f00\u53d1\u7684\u8f6f\u4ef6\uff0c\u73b0\u5728\u662fSMRT Link\u8f6f\u4ef6\u7684\u4e00\u90e8\u5206\uff0c\u7528\u4e8e\u5bf9Pacbio Long Reads\u6570\u636e\u8fdb\u884c\u5206\u6790\u3002\u51762.3\u7248\u672c\u4ec5\u80fd\u7528\u4e8e\u5bf9Pacbio RSII\u6d4b\u5e8f\u4eea\u83b7\u5f97\u7684h5\u683c\u5f0f\u6d4b\u5e8f\u6570\u636e\u8fdb\u884c\uff0c\u8be5\u7248\u672c\u6301\u7eed\u4e86\u8f83\u957f\u4e00\u6bb5\u65f6\u95f4\u3002\u540e\u6765Pacbio\u6d4b\u5e8f\u4eea\u589e\u6dfbSequel\u5e73\u53f0\u540e\uff0cSMRT Analysis\u8f6f\u4ef6\u66f4\u65b0\u52303.0\uff0c\u589e\u52a0\u652f\u6301\u5bf9Pacbio Sequel\u6d4b\u5e8f\u4eea\u83b7\u5f97\u7684bam\u683c\u5f0f\u6570\u636e\u8fdb\u884c\u5206\u6790\u3002\u73b0\u5728\uff082018.09.02\uff09\u6700\u65b0\u7248\u672c\u7684SMRT Analysis\u5230\u4e865.1\u7248\u672c\u3002<\/p>\n<h1>2. \u4e0b\u8f7d\u5e76\u5b89\u88c5SMRT Link\u8f6f\u4ef6<\/h1>\n<p>\u5c06SMRT Link\u5b89\u88c5\u5230CentOS 6.9\u7cfb\u7edf\u4e2d\u3002\u5b89\u88c5\u8f6f\u4ef6\u524d\u9700\u8981\u505a\u4e00\u4e9b\u51c6\u5907\uff1a<\/p>\n<pre>\r\n\u9996\u5148\uff0c\u786e\u5b9a\u4e3b\u673a\u540d\u662flocalhost\u5e76\u6307\u5411127.0.0.1\u7684IP\u5730\u5740\u3002\u521a\u5b89\u88c5\u5b8c\u6bd5\u7684\u7cfb\u7edf\u4e00\u822c\u90fd\u6ee1\u8db3\u6b64\u8981\u6c42\u3002\r\n\u4fdd\u8bc1\/etc\/hosts\u6587\u4ef6\u4e2d\u542b\u6709\u4ee5\u4e0b\u4e00\u884c\u4fe1\u606f\uff1a\r\n127.0.0.1    localhost\r\n\r\n\u5176\u6b21\uff0c\u4fee\u6539\/etc\/security\/limits.conf\u6587\u4ef6\uff0c\u5c3e\u90e8\u589e\u6dfb\u5982\u4e0b4\u884c\uff1a\r\nchenlianfu      soft    nproc   10240\r\nchenlianfu      hard    nproc   102400\r\nchenlianfu      soft    nofile  10240   \r\nchenlianfu      hard    nofile  102400\r\n\u6ce8\u610fchenlianfu\u662f\u5b89\u88c5SMRT Analysis\u8f6f\u4ef6\u6240\u4f7f\u7528\u7684\u7528\u6237\u7684\u7528\u6237\u540d\u3002\r\n\u8be5\u6b65\u9aa4\u7528\u4e8e\u589e\u52a0chenlianfu\u7528\u6237\u7684\u6743\u9650\uff0c\u8fd9\u662f\u4e0eSMRT\u8f6f\u4ef6\u8f83\u9ad8\u7684\u8d44\u6e90\u6d88\u8017\u548c\u8f83\u591a\u7684\u5e76\u884c\u5316\u76f8\u5173\u7684\u3002\r\n\u6b64\u5916\uff0c\u6ce8\u610f\u6b64\u6b65\u9aa4\u8fc7\u540e\uff0c\u4ece\u65b0\u767b\u9646\r\n\r\n\u7136\u540e\uff0c\u4fee\u6539\/etc\/sysconfig\/iptables\u6587\u4ef6\uff0c\u589e\u52a05432\uff08PostGresql\u6570\u636e\u5e93\u9700\u8981\uff09\u30019090\u548c8243\uff08\u8f6f\u4ef6\u7f51\u9875\u7aef\u4f7f\u7528tomcat\u63d0\u4f9b\u670d\u52a1\u65f6\u9700\u89819090\u548c8423\uff09\u7aef\u53e3\u3002\u5728\u8be5\u6587\u4ef6\u4e2d\u6b63\u786e\u7684\u4f4d\u7f6e\u589e\u52a0\u5982\u4e0b\u4e24\u884c\uff1a\r\n-A INPUT -m state --state NEW -m tcp -p tcp --dport 5432 -j ACCEPT\r\n-A INPUT -m state --state NEW -m tcp -p tcp --dport 9090 -j ACCEPT\r\n-A INPUT -m state --state NEW -m tcp -p tcp --dport 8243 -j ACCEPT\r\n\u7136\u540e\u91cd\u542f\u9632\u706b\u5899\uff0c\u8ba9\u4fee\u6539\u751f\u6548\uff1a\r\n# \/etc\/init.d\/iptables restart\r\n\r\n\u6700\u540e\uff0c\u542f\u52a8PostGresql\u6570\u636e\u5e93\u3002\r\n# \/etc\/init.d\/postgresql initdb\r\n# \/etc\/init.d\/postgresql start\r\n# chkconfig postgresql on\r\n<\/pre>\n<p>\u4ecePacbio Science\u5b98\u7f51\u4e0b\u8f7d<a href=\"https:\/\/www.pacb.com\/support\/software-downloads\/\" rel=\"noopener\" target=\"_blank\">SMRT Link\u8f6f\u4ef6<\/a>\u3002<\/p>\n<pre>\r\n\u5c06SMRT Link\u5b89\u88c5\u5230 ~\/biosoft \u76ee\u5f55\u4e0b\r\n$ mkdir ~\/biosoft\r\n$ cd ~\/biosoft\r\n$ wget https:\/\/downloads.pacbcloud.com\/public\/software\/installers\/smrtlink_5.1.0.26412.zip\r\n$ unzip smrtlink_5.1.0.26412.zip\r\n    \u8981\u6c42\u8f93\u5165\u5bc6\u7801\uff0c\u53ef\u4ee5\u4ece\u4e0b\u8f7d\u8be5\u8f6f\u4ef6\u7684\u7f51\u9875\u4e2d\u627e\u5230\u3002\r\n$ .\/smrtlink_5.1.0.26412.run\r\n    \u6839\u636e\u63d0\u793a\u4e00\u6b65\u4e00\u6b65\u8fdb\u884c\u914d\u7f6e\uff0c\u57fa\u672c\u90fd\u662f\u76f4\u63a5\u4f7f\u7528\u9ed8\u8ba4\u503c\uff0c\u6309Enter\u952e\u5373\u53ef\u3002\r\n    \u8bbe\u7f6e\u8f6f\u4ef6\u4e34\u65f6\u6587\u4ef6\u5939\u7684\u65f6\u5019\uff0c\u8981\u9009\u62e9\u4e00\u4e2a\u8f83\u5927\u5206\u533a\u6240\u5bf9\u5e94\u7684\u76ee\u5f55\u3002\u6211\u5c06\u5176\u8bbe\u7f6e\u4e3a\/home\/chenlianfu\/biosoft\/tmp\/smrtlink\r\n$ \/home\/chenlianfu\/biosoft\/smrtlink\/admin\/bin\/services-start\r\n    \u542f\u52a8SMRT Link\u8f6f\u4ef6\u3002\r\n<\/pre>\n<h1>3. \u4f7f\u7528HGAP4\u8fdb\u884c\u57fa\u56e0\u7ec4De novo\u7ec4\u88c5<\/h1>\n<pre>\r\n1. SMRT Link\u8f6f\u4ef6\u5fc5\u987b\u8981\u5728Chrome\u6d4f\u89c8\u5668\u4e2d\u6253\u5f00\u3002\u5728Chrome\u6d4f\u89c8\u5668\u4e2d\u8f93\u5165\u5b89\u88c5\u6709SMRT Link\u8f6f\u4ef6\u673a\u5668\u7684IP\u5730\u5740\uff0c\u5e76\u63a5:9090\uff0c\u4f8b\u5982\uff1a192.168.30.1:9090\uff0c\u5c31\u53ef\u4ee5\u8fde\u63a5\u5230\u8f6f\u4ef6\u7684\u7528\u6237\u767b\u9646\u754c\u9762\uff0c\u8f93\u5165\u7528\u6237\u540dadmin\uff0c\u5bc6\u7801admin\u5219\u4f1a\u8fdb\u5165\u8f6f\u4ef6\u3002\r\n\r\n2. \u70b9\u51fbData Management\uff0c\u518d\u70b9\u51fbVIEW OR IMPORT SEQUENCE DATA\uff0c\u70b9\u51fbIMPORT\u5e76\u4ece\u4e0b\u62c9\u83dc\u5355\u4e2d\u70b9\u51fbSequel Sequence Data\uff0c\u4ece\u5f39\u51fa\u7684\u6d4f\u89c8\u8bbe\u7f6e\u4e2d\u9009\u62e9\u8def\u5f84\/home\/chenlianfu\/biosoft\/smrtlink\/install\/smrtlink-release_5.1.0.26412\/bundles\/smrtinub\/install\/smrtinub-release_5.1.0.25847\/private\/pacbio\/canneddata\/lambdaTINY\/m150404_101626_42267_c100807920800000001823174110291514_s1_p0.subreadset.xml\uff0c\u70b9\u51fbIMPORT\uff0c\u8fd0\u884c\u4e00\u6bb5\u65f6\u95f4\u540e\uff0c\u5bfc\u5165\u6570\u636e\u6210\u529f\u3002\r\n\r\n3. \u8fd4\u56de\u5230\u8f6f\u4ef6\u4e3b\u754c\u9762\uff0c\u70b9\u51fbSMRT Analysis\uff0c\u70b9\u51fbCREATE NEW ANALYSIS\uff0c\u5728Analysis Application\u4e0b\u62c9\u83dc\u5355\u4e2d\u9009\u62e9Assembly(HGAP 4)\uff0cAnalysis Name\u680f\u968f\u4fbf\u586b\u5199\u5b57\u7b26\u4e32Lambda_HGAP4\uff0c\u5728Genome Length\u680f\u5c06\u57fa\u56e0\u7ec4\u5927\u5c0f\u4fee\u6539\u4e3a58000\uff0c\u5728Data Sets\u4e2d\u52fe\u9009lambda\/007_tiny\uff0c\u6700\u540e\u70b9\u51fbSTART\uff0c\u5f00\u59cb\u7a0b\u5e8f\u8fd0\u884c\u3002\r\n\r\n4. \u503c\u5f97\u6ce8\u610f\u7684\u662f\u516c\u53f8\u7ed9\u7684\u6d4b\u5e8f\u6570\u636e\u6587\u4ef6\u5939\u4e2d\u5e38\u5e38\u4e0d\u5305\u542bsts.xml\u3001adapters.fasta\u548cscraps bam\u7b49\u6587\u4ef6\uff0c\u800c\u5728\u603b\u7684xml\u6587\u4ef6\u4e2d\u5374\u5305\u542b\u4e86\u8fd9\u4e9b\u4fe1\u606f\uff0c\u9700\u8981\u5c06\u5176\u5bf9\u5e94\u7684\u884c\uff08\u7b2c7\u884c\u5230\u7b2c15\u884c\uff09\u5220\u9664\u6389\u540e\u518d\u8fd0\u884cHGAP4\uff0c\u5426\u5219\u7a0b\u5e8f\u8fd0\u884c\u4f1a\u5931\u8d25\u3002\r\n\r\n5. \u7a0b\u5e8f\u8fd0\u884c\u7ed3\u679c\u5728\/home\/chenlianfu\/biosoft\/smrtlink\/userdata\/jobs_root\/\u76ee\u5f55\u4e0b\u7684\u4e00\u4e2a\u6570\u5b57\u7f16\u53f7\uff08\u6309\u8fd0\u884c\u987a\u5e8f\u4ece000001\u5f00\u59cb\u7f16\u53f7\uff09\u7684\u6587\u4ef6\u5939\u4e2d\u3002\u8be5\u6587\u4ef6\u5939\u4e2d\u7684\u7684\u4e3b\u8981\u7ed3\u679c\u6587\u4ef6\uff08\u4e5f\u53ef\u4ee5\u5728\u7f51\u9875\u4e2d\u4e0b\u8f7d\uff09\uff1a\r\n.\/tasks\/pbcoretools.tasks.contigset2fasta-0\/file.fasta \u6700\u7ec8\u7684\u57fa\u56e0\u7ec4\u7ec4\u88c5\u7ed3\u679c\u3002\r\n.\/tasks\/pbcoretools.tasks.gather_fasta-1\/file.fasta \u6309\u67d0\u4e2a\u957f\u5ea6\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. SMRT Analysis\u7b80\u4ecb SMRT Analysis\u8f6f\u4ef6\u662f\u7531Pacb &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2618\">\u7ee7\u7eed\u9605\u8bfb <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[1],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2618"}],"collection":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=2618"}],"version-history":[{"count":13,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2618\/revisions"}],"predecessor-version":[{"id":2631,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2618\/revisions\/2631"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2618"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2618"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2618"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}