{"id":35170,"date":"2023-05-14T13:42:39","date_gmt":"2023-10-21T11:05:21","guid":{"rendered":"https:\/\/www.silicloud.com\/zh\/blog\/funannotate%e7%9a%84%e4%bd%bf%e7%94%a8%e6%ad%a5%e9%aa%a4%e5%a4%87%e5%bf%98%e5%bd%95\/"},"modified":"2024-04-30T04:07:29","modified_gmt":"2024-04-29T20:07:29","slug":"funannotate%e7%9a%84%e4%bd%bf%e7%94%a8%e6%ad%a5%e9%aa%a4%e5%a4%87%e5%bf%98%e5%bd%95","status":"publish","type":"post","link":"https:\/\/www.silicloud.com\/zh\/blog\/funannotate%e7%9a%84%e4%bd%bf%e7%94%a8%e6%ad%a5%e9%aa%a4%e5%a4%87%e5%bf%98%e5%bd%95\/","title":{"rendered":"Funannotate\u7684\u4f7f\u7528\u6b65\u9aa4[\u5907\u5fd8\u5f55]"},"content":{"rendered":"<p>\u7531\u4e8e\u5728\u5c06\u771f\u83cc\u57fa\u56e0\u7ec4\u6ce8\u91ca\u7ba1\u9053Funannotate\u5bfc\u5165Mac mini\u65f6\u9047\u5230\u56f0\u96be\u4e14\u65e0\u6cd5\u8fd0\u884c\uff0c\u56e0\u6b64\u5c06\u5176\u4f5c\u4e3a\u5907\u5fd8\u5f55\u6574\u7406\u3002(2022\/8\/1\u66f4\u65b0\uff0c2023\/1\/24\u66f4\u65b0\uff0c\u89c1\u672c\u9875\u9762\u5e95\u90e8)<\/p>\n<p>\u8bf7\u53c2\u8003\u4ee5\u4e0b\u5173\u4e8eFunannotate\u7684\u4fe1\u606f\u3002<\/p>\n<p>&nbsp;<\/p>\n<h4>\u4f7f\u7528\u8fc7\u7684\u7535\u8111<\/h4>\n<p>\u6211\u4f7f\u7528docker\u5c06Funannotate\u5b89\u88c5\u5728Mac mini (2018)[macOS Mojave]\u4e0a\u3002<\/p>\n<h4>\u6309\u7167 GitHub \u7684\u63cf\u8ff0\u6765\u770b\uff0c\u5b83\u65e0\u6cd5\u8fd0\u884c\u3002<\/h4>\n<p>\u5728GitHub\u7684\u8bf4\u660e\u4e2d\uff0c\u4f7f\u7528Docker\u8fdb\u884c\u5b89\u88c5\u5982\u4e0b\u3002<\/p>\n<pre class=\"post-pre\"><code># download\/pull the image from docker hub\r\n$ docker pull nextgenusfs\/funannotate\r\n\r\n# download bash wrapper script (optional)\r\n$ wget -O funannotate-docker https:\/\/raw.githubusercontent.com\/nextgenusfs\/funannotate\/master\/funannotate-docker\r\n\r\n# might need to make this executable on your system\r\n$ chmod +x \/path\/to\/funannotate-docker\r\n\r\n# assuming it is in your PATH, now you can run this script as if it were the funannotate executable script\r\n$ funannotate-docker test -t predict --cpus 12\r\n<\/code><\/pre>\n<p>\u5982\u679c\u4f7f\u7528\u8fd9\u4e2a\uff0c\u5c31\u53ef\u4ee5\u8fdb\u884c\u5b89\u88c5\uff0c\u867d\u7136\u53ef\u4ee5\u8fd0\u884c\uff0c\u4f46\u662f\u5c1d\u8bd5\u6267\u884cfunannotate-docker predict\u7684\u65f6\u5019\uff0c<\/p>\n<pre class=\"post-pre\"><code>CMD ERROR: trainGlimmerHMM\r\n\r\n~\u7701\u7565~\r\n\r\nb\"Cnat't locate Getopt\/Std.pm in @INC (you may need to install the Getopt::Std module)\r\n<\/code><\/pre>\n<p>\u51fa\u73b0\u9519\u8bef\u540e\uff0c\u5b83\u5c31\u505c\u6b62\u8fd0\u884c\u4e86\u3002<br \/>\n\u901a\u8fc7\u9605\u8bfb\u9519\u8bef\u4fe1\u606f\u5f97\u77e5\uff0c\u7f3a\u5c11 prel \u6a21\u5757\uff0c\u4f46\u7531\u4e8e\u4f7f\u7528\u4e86 Docker\uff0c\u4e0d\u77e5\u9053\u8be5\u5982\u4f55\u6dfb\u52a0\u6a21\u5757\u2026\uff08\u5982\u679c\u6709\u4eba\u77e5\u9053\u89e3\u51b3\u529e\u6cd5\uff0c\u8bf7\u544a\u8bc9\u6211\uff09\u3002<\/p>\n<h4>\u89e3\u51b3\u65b9\u6cd5 (ji\u011b ju\u00e9 f\u01ce)<\/h4>\n<p>\u5728\u4f7f\u7528Docker\u9032\u884c\u5c0e\u5165\u6642\uff0c<\/p>\n<pre class=\"post-pre\"><code># download\/pull the image from docker hub\r\n$ docker pull nextgenusfs\/funannotate\r\n<\/code><\/pre>\n<p>\u5c3d\u7ba1\u4ee5\u524d\u8ba4\u4e3a\u53ea\u6709\u4e00\u4e2a\u7248\u672c\uff0c\u5b9e\u9645\u4e0a\u8fd8\u5b58\u5728\u53e6\u4e00\u4e2a\u7248\u672c\u3002<\/p>\n<p>&nbsp;<\/p>\n<p>\u5f53\u6211\u6d4f\u89c8Docker Hub\u7f51\u7ad9\u65f6\uff0c<\/p>\n<pre class=\"post-pre\"><code>docker pull nextgenusfs\/funannotate:latest\r\n<\/code><\/pre>\n<p>\u4ee5\u53ca<br \/>\n(Translation: And)<\/p>\n<pre class=\"post-pre\"><code>docker pull nextgenusfs\/funannotate:v1.8.9\r\n<\/code><\/pre>\n<p>\u5b58\u5728\u4e24\u4e2a\u7248\u672c\u3002<br \/>\n\u6309\u7167GitHub\u7684\u8bf4\u660e\u6267\u884cdocker pull\u547d\u4ee4\u65f6\uff0c\u53ef\u80fd\u4f7f\u7528\u7684\u662flatest\u7248\u672c\u3002<\/p>\n<p>\u56e0\u6b64\uff0c<\/p>\n<pre class=\"post-pre\"><code>$ docker pull nextgenusfs\/funannotate:v1.8.9\r\n\r\n$ wget -O funannotate-docker https:\/\/raw.githubusercontent.com\/nextgenusfs\/funannotate\/master\/funannotate-docker\r\n\r\n$ chmod +x \/path\/to\/funannotate-docker\r\n\r\n$ funannotate-docker test -t predict --cpus 12\r\n<\/code><\/pre>\n<p>\u6309\u7167\u8fd9\u4e2a\u6b65\u9aa4\u6210\u529f\u5b89\u88c5\u4e86Funannotate v1.8.9\u540e\uff0c\u6d41\u6c34\u7ebf\u5f00\u59cb\u8fd0\u884c\u3002<br \/>\n\u4e0d\u77e5\u9053v1.8.9\u548clatest\u4e4b\u95f4\u6709\u4ec0\u4e48\u533a\u522b\uff0c\u4f46\u662f\u5982\u679clatest\u65e0\u6cd5\u8fd0\u884c\uff0c\u4e5f\u8bb8\u5b89\u88c5\u4e0a\u4e00\u4e2a\u7248\u672c\u53ef\u4ee5\u4f7f\u5176\u8fd0\u884c\u3002<\/p>\n<h4>\u8d3b\u7b11\u5927\u65b9<\/h4>\n<p>\u6211\u6210\u529f\u5730\u5c0e\u5165\u4e86\u7121\u4e8bFunannotate pipeline\u4e26\u6309\u7167\u6559\u7a0b\u4e2d\u7684Genome assembly and RNA-seq\u9032\u884c\u4e86\u5206\u6790\u3002<\/p>\n<p>&nbsp;<\/p>\n<p>\u6211\u5df2\u7ecf\u5b8c\u6210\u4e86\u4ee5\u4e0b\u6240\u6709\u5fc5\u8981\u7684\u5de5\u4f5c\u3002<\/p>\n<pre class=\"post-pre\"><code>funannotate-docker clean\r\nfunannotate-docker sort\r\nfunannotate-docker mask\r\nfunannotate-docker train\r\nfunannotate-docker predict\r\nfunannotate-docker update\r\nfunannotate-docker annotate\r\n<\/code><\/pre>\n<p>\u7136\u800c\uff0c\u4ee5\u4e0b\u53ef\u9009\u7684\u4efb\u52a1\u51fa\u73b0\u9519\u8bef\uff0c\u65e0\u6cd5\u5b8c\u6210\u3002<\/p>\n<pre class=\"post-pre\"><code>funannotate-docker remote -i fun -m phobius -e your-email@domain.edu\r\nfunannotate-docker iprscan -i fun -m docker --cpus 12\r\nfunannotate-docker remote -i fun -m antismash -e your-email@domain.edu\r\n<\/code><\/pre>\n<p>\u6216\u8bb8\u662f\u7531\u4e8eRNA-seq\u6570\u636e\u8d28\u91cf\u7684\u95ee\u9898\uff0c\u4e0e\u4f7f\u7528FunGAP pipeline\uff08\u8bf7\u53c2\u8003\u4ee5\u4e0b\u7f51\u7ad9\uff09\u76f8\u6bd4\uff0c\u9884\u6d4b\u51fa\u7684\u57fa\u56e0\u6570\u91cf\u589e\u52a0\u4e865000\u4e2a\u4ee5\u4e0a\u3002<br \/>\n\u901a\u8fc7\u6539\u53d8\u9884\u6d4b\u65f6\u7684\u6bd4\u91cd\uff0c\u662f\u5426\u53ef\u4ee5\u6539\u5584\u60c5\u51b5\u5462\uff1f<br \/>\n\uff08\u5b9e\u9645\u4e0a\uff0c\u9884\u6d4b\u65f6\u7684\u6bd4\u91cd\u80fd\u591f\u88ab\u6539\u53d8\u5417&#8230;\uff1f\uff09<\/p>\n<p>&nbsp;<\/p>\n<p>\u8bf7\u7528\u4e2d\u6587\u8fdb\u884c\u4ee5\u4e0b\u53e5\u5b50\u7684\u672c\u5730\u5316\u6539\u5199\uff0c\u53ea\u9700\u8981\u7ed9\u51fa\u4e00\u4e2a\u9009\u9879\uff1a<\/p>\n<p>\u53ef\u4ee5\u4f60\u5e2e\u6211\u627e\u4e00\u672c\u4e66\u5417\uff1f<\/p>\n<blockquote><p>2022\u5e748\u67081\u65e5\u8865\u5145<\/p><\/blockquote>\n<p>\u52302022\u5e747\u670830\u65e5\uff0c\u5df2\u7ecf\u51fa\u73b0\u4e86\u65b0\u7248\u672c(v1.8.12)\u3002<\/p>\n<p>&nbsp;<\/p>\n<p>\u786e\u8ba4\u5728v1.8.12\u7248\u672c\u4e2d\uff0c\u4e0e1.8.9\u7248\u672c\u4e00\u6837\u6b63\u5e38\u8fd0\u884c\u3002<br \/>\n\u7136\u800c\uff0c\u5c1d\u8bd5\u5728remote\u4e0a\u8fd0\u884cinterproscan\u548cantismash\u65f6\u4ecd\u7136\u65e0\u6cd5\u6b63\u5e38\u5de5\u4f5c\uff0c\u540c\u65f6\u5c1d\u8bd5\u5c06geneMark\u6dfb\u52a0\u5230predict\u4e2d\uff0c\u4f46\u4e5f\u6ca1\u6709\u6210\u529f\u3002<\/p>\n<p>\u5173\u4e8eantismash\uff0c\u53ef\u4ee5\u4f7f\u7528WEB\u7248\u672c\uff1b\u5173\u4e8einterproscan\uff0c\u53ef\u4ee5\u4f7f\u7528docker\u8fdb\u884c\u8fd0\u884c\uff0c\u5e76\u5206\u522b\u4f7f\u7528gbk\u6587\u4ef6\u548cxml\u6587\u4ef6\u4f5c\u4e3afunannotate\u7684annotate\u8f93\u5165\uff0c\u770b\u8d77\u6765\u5e94\u8be5\u6ca1\u6709\u95ee\u9898\u3002<\/p>\n<p>Antismash\u5728\u4ee5\u4e0b\u7f51\u7ad9\u4e0a\u8fdb\u884c\u4e86\u5206\u6790\u3002<\/p>\n<p>&nbsp;<\/p>\n<p>interproscan\u4f7f\u7528\u4e86blaxterlab\/interproscan\u955c\u50cf\u3002<\/p>\n<p>&nbsp;<\/p>\n<p>\u8bf7\u7ed9\u6211\u4e00\u4e2a\u4e2d\u56fd\u540d\u5b57\u3002<\/p>\n<blockquote><p>2023\u5e741\u670824\u65e5\u8865\u5145\u8bb0\u5f55<\/p><\/blockquote>\n<p>2023\u5e741\u670824\u65e5\u73b0\u5728\uff0c\u5df2\u7ecf\u6709\u4e00\u4e2a\u66f4\u65b0\u7684\u7248\u672c\u53d1\u5e03\u4e86\uff08v1.8.14\uff09\u3002<\/p>\n<p>&nbsp;<\/p>\n<p>\u548cv1.8.12\u4e00\u6837\uff0c\u4ee5\u4e0b\u95ee\u9898\u4e5f\u88ab\u89c2\u5bdf\u5230\u3002<br \/>\n\u2192\u5728\u8fdc\u7a0b\u4e0a\u65e0\u6cd5\u8fd0\u884cinterproscan\u6216antismash\u3002<br \/>\n\u2192\u65e0\u6cd5\u5728geneMark\u4e0a\u8fd0\u884cpredict\u3002<\/p>\n<p>\u5728\u4f7f\u7528Web\u7248\u7684antiSmash\u65f6\uff0c\u53d1\u73b0\u5982\u679c\u5728FUN_00001\u57fa\u56e0\u4e2d\u5305\u542b\u4e86FUN_00001-T1\u3001FUN_00001-T2\u7b49\u526a\u63a5\u53d8\u4f53\u7684\u4fe1\u606f\uff0c\u7a0b\u5e8f\u5c31\u65e0\u6cd5\u8fd0\u884c\u3002<br \/>\n\u4f3c\u4e4e\u5982\u679c\u5b58\u5728\u526a\u63a5\u53d8\u4f53\uff0c\u6bcf\u4e2a\u53d8\u4f53\u90fd\u4f1a\u88ab\u8ba4\u4e3a\u662f\u4e0d\u540c\u7684\u57fa\u56e0\uff0c\u4e5f\u5c31\u662f\u8bf4\uff0c\u5982\u679c\u5728\u540c\u4e00\u533a\u57df\u5b58\u5728\u4e24\u4e2a\u57fa\u56e0\uff0c\u7a0b\u5e8f\u5c31\u4f1a\u5931\u6548\u3002<\/p>\n<p>\u5728\u4f7f\u7528Funannotate\u8fdb\u884c\u6ce8\u91ca\u65f6\uff0c\u5982\u679c\u5b58\u5728\u4e0d\u5305\u542b\u53d8\u5f02\u7684\u8bbe\u7f6e\uff0c\u4f3c\u4e4e\u53ef\u4ee5\u901a\u8fc7remote\u9009\u9879\u8fd0\u884c\u3002<br \/>\n\uff08\u662f\u5426\u5b58\u5728\u4e0d\u5305\u542b\u53d8\u5f02\u7684\u8bbe\u7f6e\uff1f\uff09<\/p>\n<blockquote><p>2023\u5e749\u670818\u65e5\u9644\u8a00<\/p><\/blockquote>\n<p>\u6700\u8fd1\u6211\u4f7f\u7528Funannotate\u65f6\u6ce8\u610f\u5230\u7684\u95ee\u9898\u662f\uff0c\u7edd\u5bf9\u4e0d\u80fd\u5728\u5b58\u50a8\u60f3\u8981\u5206\u6790\u7684fasta\u6587\u4ef6\u7b49\u7684\u76ee\u5f55\u540d\u79f0\u4e2d\u6dfb\u52a0\u7a7a\u683c\u3002\u5982\u679c\u6dfb\u52a0\u4e86\u7a7a\u683c\uff0cBUSCO\u4f1a\u51fa\u73b0\u6545\u969c\u800c\u65e0\u6cd5\u8fd0\u884c\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u7531\u4e8e\u5728\u5c06\u771f\u83cc\u57fa\u56e0\u7ec4\u6ce8\u91ca\u7ba1\u9053Funannotate\u5bfc\u5165Mac mini\u65f6\u9047\u5230\u56f0\u96be\u4e14\u65e0\u6cd5\u8fd0\u884c\uff0c\u56e0\u6b64\u5c06\u5176\u4f5c\u4e3a\u5907\u5fd8\u5f55\u6574 [&hellip;]<\/p>\n","protected":false},"author":10,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-35170","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"yoast_head":"<!-- This site is optimized with the Yoast SEO Premium plugin v21.5 (Yoast SEO v21.5) - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Funannotate\u7684\u4f7f\u7528\u6b65\u9aa4[\u5907\u5fd8\u5f55] - Blog - Silicon Cloud<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.silicloud.com\/zh\/blog\/funannotate\u7684\u4f7f\u7528\u6b65\u9aa4\u5907\u5fd8\u5f55\/\" \/>\n<meta property=\"og:locale\" content=\"zh_CN\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Funannotate\u7684\u4f7f\u7528\u6b65\u9aa4[\u5907\u5fd8\u5f55]\" \/>\n<meta property=\"og:description\" content=\"\u7531\u4e8e\u5728\u5c06\u771f\u83cc\u57fa\u56e0\u7ec4\u6ce8\u91ca\u7ba1\u9053Funannotate\u5bfc\u5165Mac mini\u65f6\u9047\u5230\u56f0\u96be\u4e14\u65e0\u6cd5\u8fd0\u884c\uff0c\u56e0\u6b64\u5c06\u5176\u4f5c\u4e3a\u5907\u5fd8\u5f55\u6574 [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.silicloud.com\/zh\/blog\/funannotate\u7684\u4f7f\u7528\u6b65\u9aa4\u5907\u5fd8\u5f55\/\" \/>\n<meta property=\"og:site_name\" content=\"Blog - Silicon Cloud\" \/>\n<meta property=\"article:published_time\" content=\"2023-10-21T11:05:21+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-04-29T20:07:29+00:00\" \/>\n<meta name=\"author\" content=\"\u5b87, \u534e\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"\u4f5c\u8005\" \/>\n\t<meta name=\"twitter:data1\" content=\"\u5b87, \u534e\" 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