{"id":67112,"date":"2026-11-14T19:47:56","date_gmt":"2026-11-14T11:47:56","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=67112"},"modified":"2026-11-14T19:53:17","modified_gmt":"2026-11-14T11:53:17","slug":"reproduce-tofu-maapo-metagenome-benchmark","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/reproduce-tofu-maapo-metagenome-benchmark\/","title":{"rendered":"\u540c\u6837\u7684 100 \u4efd\u7caa\u4fbf\u5b8f\u57fa\u56e0\u7ec4\uff0c\u4e3a\u4ec0\u4e48\u591a\u51fa 1,197 \u4e2a bin\uff1f\u590d\u73b0 TOFU-MAaPO \u56fe 2"},"content":{"rendered":"
\n

\u540c\u4e00\u6279\u80a0\u9053\u6d4b\u5e8f\u6570\u636e\uff0cTOFU-MAaPO \u7684\u66f2\u7ebf\u4e0a\u6709 2,745 \u4e2a bin\uff0cATLAS \u6709 1,548 \u4e2a\u3002\u591a\u51fa\u7684 1,197 \u4e2a\u7a76\u7adf\u4ee3\u8868\u4ec0\u4e48\uff1f\u6253\u5f00\u4f5c\u8005\u7684 CheckM \u8868\uff0c\u628a\u8d28\u91cf\u95e8\u69db\u6362\u4e00\u6b21\uff0c\u5355\u662f ATLAS \u7684\u6570\u5b57\u5c31\u4f1a\u4ece 1,548 \u53d8\u6210 1,458\u3002\u505a\u83cc\u7fa4\u57fa\u56e0\u7ec4\u76ee\u5f55\u65f6\uff0c\u5148\u628a\u201c\u4e00\u4e2a bin \u600e\u6837\u83b7\u5f97\u5165\u573a\u8d44\u683c\u201d\u8bf4\u6e05\u695a\uff0c\u540e\u9762\u7684\u6bd4\u8f83\u624d\u6709\u610f\u4e49\u3002Wacker \u7b49\uff0cNature Communications\uff0c2026\uff0c\u56fe 2<\/a><\/p>\n

\"\u56db\u5957\u6d41\u7a0b\u5728\u540c\u4e00\u767e\u4efd\u6837\u672c\u4e2d\u7684\u6b63\u5206<\/a><\/p>\n

\u8bba\u6587\u89e3\u51b3\u4e86\u4ec0\u4e48\u95ee\u9898<\/h2>\n

\u5b8f\u57fa\u56e0\u7ec4\u91cc\uff0c\u4e0d\u540c\u5fae\u751f\u7269\u7684 DNA \u6df7\u5728\u4e00\u8d77\u3002\u8981\u7814\u7a76\u4e00\u682a\u83cc\u53ef\u80fd\u643a\u5e26\u54ea\u4e9b\u57fa\u56e0\uff0c\u5355\u6709\u7269\u79cd\u4e30\u5ea6\u8868\u8fd8\u4e0d\u591f\u3002\u7ec4\u88c5\u5148\u628a\u77ed\u8bfb\u6bb5\u62fc\u6210\u957f\u4e00\u4e9b\u7684 contig\uff0c\u5206\u7bb1\u518d\u6309\u5e8f\u5217\u7279\u5f81\u548c\u8986\u76d6\u5ea6\u7b49\u7ebf\u7d22\uff0c\u628a\u53ef\u80fd\u6765\u81ea\u540c\u4e00\u57fa\u56e0\u7ec4\u7684 contig \u653e\u8fdb\u4e00\u4e2a bin\u3002\u7ecf\u8d28\u91cf\u8bc4\u4f30\u7684\u7ec4\u88c5\u57fa\u56e0\u7ec4\u5e38\u79f0\u4e3a MAG\u3002\u4f4e\u4e30\u5ea6\u83cc\u5bb9\u6613\u62fc\u4e0d\u5168\uff0c\u8fd1\u7f18\u83cc\u53c8\u5bb9\u6613\u88ab\u5206\u5230\u4e00\u8d77\u3002<\/p>\n

\u4f5c\u8005\u628a\u516c\u5171\u6d4b\u5e8f\u6570\u636e\u4e0b\u8f7d\u3001\u8d28\u63a7\u3001\u53bb\u5bbf\u4e3b\u3001MEGAHIT \u7ec4\u88c5\u3001\u591a\u5de5\u5177\u5206\u7bb1\u3001MAGScoT \u6574\u5408\u4ee5\u53ca\u8d28\u91cf\u8bc4\u4f30\u4e32\u6210 Nextflow \u6d41\u7a0b\uff0c\u7528 50 \u4efd ME\/CFS \u60a3\u8005\u548c 50 \u4efd\u5bf9\u7167\u7684\u7caa\u4fbf\u5b8f\u57fa\u56e0\u7ec4\u540c\u65f6\u6bd4\u8f83\u56db\u5957\u5de5\u5177\u3002\u65b9\u6cd5\u4e0a\u7684\u4eae\u70b9\u662f\u8ba9\u591a\u4e2a\u5206\u7bb1\u5668\u5148\u7ed9\u51fa\u5019\u9009\uff0c\u518d\u51ed\u6807\u8bb0\u57fa\u56e0\u7b49\u8bc1\u636e\u7b5b\u9009\u548c\u6574\u5408\u3002\u6bcf\u4e2a\u7b97\u6cd5\u4ea4\u51fa\u591a\u5c11 bin\u3001\u6574\u5408\u540e\u7559\u4e0b\u591a\u5c11\u3001\u7edf\u4e00\u8bc4\u5206\u540e\u8fd8\u80fd\u4fdd\u7559\u591a\u5c11\uff0c\u662f\u4e09\u4e2a\u4e0d\u540c\u7684\u95ee\u9898\u3002\u8bba\u6587\u65b9\u6cd5<\/a> \u00b7 1.6.0 \u6d41\u7a0b\u6e90\u7801<\/a><\/p>\n

\u7b2c\u4e00\u6b65\u3000\u53d6\u56de\u4f5c\u8005\u7528\u4e8e\u56fe 2 \u7684\u6587\u4ef6<\/h2>\n

\u4e0b\u9762\u7684\u8f7b\u91cf\u590d\u73b0\u53ea\u9700\u8981 Git \u548c Python 3\uff0c\u4e0d\u4e0b\u8f7d FASTQ\u3002\u89e3\u538b\u672c\u6587\u811a\u672c\u5305\uff0c\u5728\u542b recount.py<\/code> \u7684\u76ee\u5f55\u6267\u884c\u4e0b\u5217\u547d\u4ee4\u3002\u4ed3\u5e93\u56fa\u5b9a\u5230\u5177\u4f53\u63d0\u4ea4\uff0c\u4fdd\u8bc1\u8bfb\u53d6\u7684\u662f\u672c\u6587\u6838\u5bf9\u8fc7\u7684\u90a3\u4e00\u7248\u8868\u683c\u548c\u77e2\u91cf\u56fe\u3002\u4e0b\u8f7d\u590d\u73b0\u811a\u672c\u548c\u9884\u671f\u8f93\u51fa<\/a> \u00b7 \u4f5c\u8005\u7684\u57fa\u51c6\u6587\u4ef6\u76ee\u5f55<\/a><\/p>\n

\n
Shell<\/span><\/div>\n
git clone https:\/\/github.com\/ikmb\/TOFUpaper.git\r\ngit -C TOFUpaper checkout 826dc7eec3eac1855bc14f60565d8206f35a1ab0\r\npython3 recount.py TOFUpaper\/assembly_benchmarks\r\n<\/code><\/pre>\n<\/div>\n
\u76ee\u5f55\u91cc\u6700\u503c\u5f97\u6253\u5f00\u7684\u4e09\u4e2a\u6587\u4ef6\u662f atlas_checkm_table.tsv<\/code>\u3001\u4ee5 00_100sample<\/code> \u5f00\u5934\u7684 R \u811a\u672c\u548c arranged_benchmark_100samples_v2.svg<\/code>\u3002\u7b2c\u4e00\u4efd\u7ed9\u51fa ATLAS \u7684\u9010\u4e2a bin \u8bc4\u5206\uff0c\u7b2c\u4e8c\u4efd\u8bf4\u660e\u6392\u5e8f\u548c\u8fc7\u6ee4\u65b9\u5f0f\uff0c\u7b2c\u4e09\u4efd\u4fdd\u5b58\u4e86\u56db\u6761\u66f2\u7ebf\u3002R \u811a\u672c\u5f00\u5934\u4f7f\u7528\u4f5c\u8005\u7684\u96c6\u7fa4\u6302\u8f7d\u76ee\u5f55\uff0c\u76f4\u63a5\u8fd0\u884c\u4f1a\u5728\u5bfb\u627e\u53e6\u5916\u51e0\u5957\u6d41\u7a0b\u7684\u8bc4\u5206\u8868\u65f6\u9047\u5230\u8def\u5f84\u95ee\u9898\u3002ATLAS \u6e90\u8868<\/a> \u00b7 \u4f5c\u8005 R \u811a\u672c\u7b2c 10\u201355 \u884c<\/a><\/p>\n
\u7b2c\u4e8c\u6b65\u3000\u4ece ATLAS \u7684\u6e90\u8868\u91cd\u7b97\u4e24\u4e2a\u6570<\/h2>\n
Completeness<\/code> \u8868\u793a\u4f30\u8ba1\u5b8c\u6574\u5ea6\uff0cContamination<\/code> \u8868\u793a\u4f30\u8ba1\u6c61\u67d3\u5ea6\u3002\u4f5c\u8005\u5bf9\u4e24\u4e2a\u767e\u5206\u6570\u4f7f\u7528 \u5b8c\u6574\u5ea6 \u2212 0.5 \u00d7 \u6c61\u67d3\u5ea6<\/code>\u3002\u4f8b\u5982\u5b8c\u6574\u5ea6 70\u3001\u6c61\u67d3\u5ea6 10 \u5f97 65 \u5206\u3002\u628a\u539f\u8868\u7684\u4e24\u5217\u4fdd\u7559\uff0c\u540e\u6765\u624d\u80fd\u8bd5\u4e0d\u540c\u9608\u503c\u3002\u53ea\u4fdd\u5b58\u6700\u7ec8\u201c\u901a\u8fc7\u201d\u6807\u8bb0\uff0c\u5c31\u65e0\u6cd5\u8ffd\u67e5\u5019\u9009\u4e3a\u4ec0\u4e48\u5165\u9009\u3002\u4f5c\u8005\u7684\u8bc4\u5206\u4e0e\u8fc7\u6ee4\u4ee3\u7801<\/a><\/p>\n
\n
Python<\/span><\/div>\n
scores = [float(row[\"Completeness\"]) - 0.5 * float(row[\"Contamination\"])\r\n          for row in bins]\r\nassert len({row[\"Bin Id\"] for row in bins}) == len(bins)\r\nprint(len(bins), sum(s > 0 for s in scores), sum(s >= 50 for s in scores))\r\n# 1548 1548 1458\r\n<\/code><\/pre>\n<\/div>\n
bins<\/code> \u662f\u811a\u672c\u8bfb\u5165\u7684 TSV \u5168\u90e8\u884c\u3002\u65ad\u8a00\u5148\u68c0\u67e5\u6bcf\u4e2a\u6807\u8bc6\u662f\u5426\u53ea\u51fa\u73b0\u4e00\u6b21\u3002\u968f\u540e\u4e24\u4e2a\u6c42\u548c\u5206\u522b\u5bf9\u5e94\u4f5c\u56fe\u7528\u7684\u6b63\u5206\u95e8\u69db\u548c\u5f52\u4e00\u5316 0.5 \u7684\u95e8\u69db\u3002\u8868\u4e2d\u7684 90 \u4e2a bin \u5206\u6570\u5927\u4e8e 0\u3001\u4f4e\u4e8e 50\u3002\u5982\u679c\u628a\u82f1\u6587\u6b63\u6587\u7684 0.5 \u76f4\u63a5\u5957\u5728\u767e\u5206\u6570\u5217\u4e0a\uff0c\u4f1a\u628a\u5927\u6279\u4f4e\u5206 bin \u8ba1\u5165\u3002<\/p>\n
\u7b2c\u4e09\u6b65\u3000\u6838\u5bf9\u56fe 2a \u7684\u56db\u6761\u66f2\u7ebf<\/h2>\n
\u4f5c\u8005\u5148\u7ed9\u6bcf\u4e2a bin \u4e00\u4e2a\u6309\u5206\u6570\u964d\u5e8f\u7684\u540d\u6b21\uff0c\u518d\u8fc7\u6ee4 score > 0<\/code>\uff0c\u7528 geom_line<\/code> \u628a\u70b9\u8fde\u8d77\u6765\u3002\u5728\u8fd9\u4e2a\u56fa\u5b9a\u7248\u672c\u7684 SVG \u4e2d\uff0c\u6bcf\u6761\u8bc4\u5206\u6298\u7ebf\u4fdd\u7559\u4e86\u6bcf\u4e2a bin \u7684\u4e00\u4e2a\u5750\u6807\u3002\u672c\u6587\u811a\u672c\u6309\u4f5c\u8005\u6307\u5b9a\u7684\u56db\u79cd\u989c\u8272\u5b9a\u4f4d\u957f\u6298\u7ebf\uff0c\u6570\u51fa\u5750\u6807\uff0c\u518d\u7528 ATLAS \u6e90\u8868\u4ea4\u53c9\u68c0\u67e5\u3002\u4e0b\u9762\u662f\u5b9e\u9645\u6267\u884c\u811a\u672c\u7684\u7ed3\u679c\u3002\u989c\u8272\u3001\u8fc7\u6ee4\u548c\u7ed8\u56fe\u4ee3\u7801<\/a> \u00b7 \u539f\u59cb SVG<\/a><\/p>\n
\n\n\n\n\n\n\n\n\n
\u6d41\u7a0b<\/th>\n\u56fe\u4e2d\u6b63\u5206 bin \u6570<\/th>\n\u672c\u6587\u600e\u6837\u6838\u5bf9<\/th>\n<\/tr>\n<\/thead>\n
TOFU-MAaPO<\/td>\n2,745<\/td>\n\u4f5c\u8005 SVG \u66f2\u7ebf\u5750\u6807\u6570<\/td>\n<\/tr>\n
metaFun<\/td>\n2,461<\/td>\n\u4f5c\u8005 SVG \u66f2\u7ebf\u5750\u6807\u6570<\/td>\n<\/tr>\n
nf-core\/mag<\/td>\n1,929<\/td>\n\u4f5c\u8005 SVG \u66f2\u7ebf\u5750\u6807\u6570<\/td>\n<\/tr>\n
ATLAS<\/td>\n1,548<\/td>\nSVG \u4e0e\u9010 bin \u7684 CheckM \u8868\u4e00\u81f4<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\u600e\u6837\u8bfb\u8fd9\u5f20\u8868\uff1f<\/strong> \u8de8\u6837\u672c\u7684\u591a\u4e2a bin \u53ef\u80fd\u5c5e\u4e8e\u540c\u4e00\u7269\u79cd\u3002\u8981\u62a5\u7269\u79cd\u6570\uff0c\u8fd8\u8981\u5b9a\u53bb\u5197\u4f59\u6807\u51c6\uff0c\u5e76\u5b9e\u9645\u805a\u7c7b\u3002\u8bba\u6587\u53e6\u62a5\u544a\u5728\u5f52\u4e00\u5316\u8bc4\u5206 \u22650.5 \u65f6\uff0cTOFU-MAaPO \u6bd4\u53e6\u5916\u4e09\u5957\u6d41\u7a0b\u5206\u522b\u591a\u51fa\u7ea6 12%\u300142%\u300177%\u3002\u90a3\u662f\u8bba\u6587\u7684\u9608\u503c\u6bd4\u8f83\u3002\u672c\u6587\u72ec\u7acb\u91cd\u7b97\u4e86 ATLAS \u7684 1,458 \u4e2a\u8fc7\u7ebf bin\uff0c\u5176\u4f59\u4e09\u5957\u5728\u672c\u8282\u6838\u5bf9\u5230\u4f5c\u56fe\u6570\u91cf\u3002\u9879\u76ee\u5982\u9700\u6309\u5b8c\u6574\u5ea6\u3001\u6c61\u67d3\u5ea6\u5206\u522b\u8bbe\u9650\uff0c\u4e5f\u5e94\u56de\u5230\u5404\u81ea\u7684\u9010 bin \u8868\u91cd\u65b0\u7b5b\u9009\u3002\u8bba\u6587\u7ed3\u679c\u4e0e\u57fa\u51c6\u8bbe\u7f6e<\/a><\/p>\n
\u8fd8\u6709\u4e00\u4e2a\u503c\u5f97\u81ea\u5df1\u52a8\u624b\u67e5\u7684\u4f8b\u5b50\u3002ATLAS \u8868\u91cc\uff0cSRR6784403_maxbin_06<\/code> \u7684\u5b8c\u6574\u5ea6\u662f 92.06%\uff0c\u6c61\u67d3\u5ea6\u9ad8\u8fbe 44.71%\uff0c\u7efc\u5408\u5206\u4ecd\u6709 69.705\u3002\u6211\u4eec\u5728\u6e90\u8868\u4e2d\u6570\u51fa 101 \u4e2a<\/strong>\u7efc\u5408\u5206\u81f3\u5c11 50\u3001\u540c\u65f6\u6c61\u67d3\u5ea6\u81f3\u5c11 10% \u7684 bin\u3002\u82e5\u4efb\u52a1\u662f\u628a\u4e00\u6761\u8010\u836f\u57fa\u56e0\u5f52\u5230\u67d0\u682a\u83cc\u540d\u4e0b\uff0c\u6df7\u5165\u5176\u4ed6\u7269\u79cd\u7684 contig \u53ef\u80fd\u8ba9\u5f52\u5c5e\u5224\u65ad\u51fa\u9519\u3002\u7b5b\u76ee\u5f55\u65f6\u53ef\u4ee5\u628a\u5b8c\u6574\u5ea6\u548c\u6c61\u67d3\u5ea6\u5404\u5217\u4e00\u680f\uff0c\u9010\u9879\u8fc7\u6ee4\uff0c\u518d\u68c0\u67e5\u76ee\u6807\u57fa\u56e0\u6240\u5728 contig \u7684\u8986\u76d6\u5ea6\u548c\u5206\u7c7b\u8bc1\u636e\u3002\u8fd9\u6837\u4e00\u6765\uff0c\u8bfb\u8005\u77e5\u9053\u54ea\u4e9b\u5019\u9009\u662f\u56e0\u4e3a\u8bc1\u636e\u4e0d\u8db3\u88ab\u5254\u9664\uff0c\u4e5f\u80fd\u6309\u81ea\u5df1\u7684\u7814\u7a76\u95ee\u9898\u91cd\u505a\u7b5b\u9009\u3002\u7528\u4e8e\u6838\u5bf9\u7684\u9010 bin \u6e90\u8868<\/a><\/p>\n
\u7b2c\u56db\u6b65\u3000\u4ece\u4e00\u4e2a\u771f\u5b9e\u6837\u672c\u5f00\u59cb\u8dd1\u7ec4\u88c5<\/h2>\n
\u5982\u679c\u4f60\u7684\u76ee\u6807\u662f\u628a\u65b9\u6cd5\u7528\u5230\u81ea\u5df1\u7684\u6d4b\u5e8f\u6570\u636e\uff0c\u4e0b\u4e00\u6b65\u624d\u9700\u8981 Linux\u3001Nextflow\u3001Java\u3001Apptainer \u6216 Singularity\uff0c\u4ee5\u53ca\u53ef\u5199\u7684\u5de5\u4f5c\u76d8\u3002\u4e0b\u9762\u9009\u53d6\u539f\u961f\u5217\u4e2d\u7684 SRR6784413<\/code> \u6f14\u793a\u542f\u52a8\u65b9\u5f0f\u3002\u672c\u6587\u5b9e\u9645\u8fd0\u884c\u5230\u4e0a\u9762\u7684\u6e90\u8868\u548c\u56fe\u6587\u4ef6\u6838\u5bf9\uff0c\u8fd9\u4e00\u8282\u7ed9\u51fa\u8bfb\u8005\u5728\u81ea\u5df1\u7684\u8282\u70b9\u4e0a\u8fd0\u884c\u7684\u547d\u4ee4\u3002\u6837\u672c\u6e05\u5355<\/a> \u00b7 \u4f5c\u8005\u8fd0\u884c 100 \u4e2a\u6837\u672c\u7684\u811a\u672c<\/a><\/p>\n
    \n
  1. \u4ece\u57fa\u51c6\u4ed3\u5e93\u590d\u5236 tofu.config<\/code>\u3002\u5c06 params.genomes.human.bowtie_index<\/code> \u6307\u5411\u4eba\u5bbf\u4e3b Bowtie2 \u7d22\u5f15\u7684\u5171\u540c\u524d\u7f00<\/strong>\uff0c\u5c06 gtdbtk_reference<\/code> \u6307\u5411\u5df2\u5b89\u88c5\u7684 R207_v2 \u6570\u636e\u3002\u4f5c\u8005\u914d\u7f6e\u542f\u7528 Singularity\uff0c\u800c custom<\/code> \u914d\u7f6e\u9ed8\u8ba4\u542f\u7528 Apptainer\u3002\u82e5\u6cbf\u7528\u4f5c\u8005\u7684 Singularity \u6bb5\uff0c\u5728\u81ea\u5df1\u7684\u914d\u7f6e\u4e2d\u5199\u5165 apptainer.enabled = false<\/code>\u3002\u82e5\u7528 Apptainer\uff0c\u628a\u5bb9\u5668\u6bb5\u6539\u4e3a apptainer<\/code> \u5e76\u53ea\u542f\u7528\u8fd9\u4e00\u79cd\u3002\u4fee\u6539 cacheDir<\/code> \u548c\u6302\u8f7d\u76ee\u5f55\uff0c\u786e\u4fdd\u5bb9\u5668\u5185\u53ef\u8bfb\u6570\u636e\u5e93\u3001\u53ef\u5199\u5de5\u4f5c\u76ee\u5f55\u3002\u6309\u8282\u70b9\u5b9e\u9645\u914d\u989d\u8bbe\u7f6e max_memory<\/code>\u3001max_cpus<\/code> \u548c\u672c\u5730\u6267\u884c\u5668\u603b\u8d44\u6e90\uff0c\u66ff\u6362\u539f\u914d\u7f6e\u4e2d\u7684 \/dpool<\/code> \u8def\u5f84\u3002\u56fa\u5b9a\u7248\u672c\u9ed8\u8ba4\u914d\u7f6e<\/a> \u00b7 \u5b89\u88c5\u4e0e\u6570\u636e\u5e93\u8bf4\u660e<\/a> \u00b7 \u5bbf\u4e3b\u7d22\u5f15\u8bf4\u660e<\/a><\/li>\n
  2. \u5728 shell \u73af\u5883\u914d\u7f6e\u81ea\u5df1\u7684 NCBI_API_KEY<\/code>\u3002\u4e0b\u9762\u4f7f\u7528\u8bba\u6587\u7248\u672c 1.6.0 \u7684\u516d\u79cd\u5206\u7bb1\u5668\uff0c\u663e\u5f0f\u5217\u51fa\u5b83\u4eec\u6709\u52a9\u4e8e\u590d\u67e5\u53c2\u6570\u3002--assemblymode single<\/code> \u6307\u6bcf\u4efd\u6837\u672c\u5206\u522b\u7ec4\u88c5\u3002\u542f\u7528 VAMB \u540e\uff0c\u5b83\u4ecd\u53ef\u5bf9\u591a\u4e2a\u6837\u672c\u8054\u5408\u5206\u7bb1\uff0c\u56e0\u6b64\u5355\u6837\u672c\u8bd5\u8dd1\u53ea\u80fd\u9a8c\u8bc1\u6d41\u7a0b\u548c\u8d44\u6e90\u6761\u4ef6\u30021.6.0 \u5b9e\u9645\u9ed8\u8ba4\u53c2\u6570<\/a> \u00b7 \u53c2\u6570\u6587\u6863<\/a><\/li>\n<\/ol>\n
    \n
    Shell<\/span><\/div>\n
    cp TOFUpaper\/assembly_benchmarks\/TOFU-MAaPO\/tofu.config .\/tofu.config\r\n# \u5148\u6309\u4e0a\u6587\u4fee\u6539 tofu.config\uff0c\u518d\u8fd0\u884c\u4ee5\u4e0b\u547d\u4ee4\r\nnextflow run ikmb\/TOFU-MAaPO -r 1.6.0 \\\r\n  -profile custom -c \"$PWD\/tofu.config\" \\\r\n  --sra SRR6784413 --apikey \"$NCBI_API_KEY\" --genome human \\\r\n  --assembly --assemblymode single \\\r\n  --binner comebin,concoct,maxbin,semibin,metabat,vamb \\\r\n  --publish_rawbins --publish_megahit \\\r\n  --outdir \"$PWD\/results-pilot\" -work-dir \"$PWD\/work-pilot\" \\\r\n  -with-trace \"$PWD\/pilot-trace.tsv\" -with-report \"$PWD\/pilot-report.html\"\r\n<\/code><\/pre>\n<\/div>\n
    \u8bd5\u8dd1\u5b8c\u6210\u540e\u5982\u4f55\u9a8c\u6536\u3002<\/strong> \u6253\u5f00 pilot-trace.tsv<\/code>\uff0c\u6309 name<\/code> \u627e\u7ec4\u88c5\u3001\u5206\u7bb1\u3001\u6574\u5408\u548c CheckM \u4efb\u52a1\uff0c\u6838\u5bf9 status<\/code>\u3001realtime<\/code> \u548c peak_rss<\/code>\u3002\u56de\u5230\u7ed3\u679c\u76ee\u5f55\u68c0\u67e5 contig\u3001\u539f\u59cb bin \u548c\u6700\u7ec8 CheckM \u8868\u662f\u5426\u90fd\u751f\u6210\u3002\u82e5\u67d0\u6b65\u5931\u8d25\uff0c\u4ece trace \u7684\u4efb\u52a1\u54c8\u5e0c\u627e\u5230\u5de5\u4f5c\u76ee\u5f55\uff0c\u8bfb .command.err<\/code>\u3002\u539f\u542f\u52a8\u76ee\u5f55\u4e2d\u7684 .nextflow\/cache<\/code> \u548c\u5de5\u4f5c\u76ee\u5f55\u90fd\u4fdd\u7559\u65f6\uff0c\u53ef\u4ee5\u7528\u540c\u4e00\u547d\u4ee4\u52a0 -resume<\/code> \u590d\u7528\u6709\u6548\u4efb\u52a1\u3002<\/p>\n
    \u600e\u6837\u6269\u5230 100 \u4efd\u3002<\/strong> \u628a --sra<\/code> \u6539\u6210 SRP102150<\/code>\uff0c\u4e3a\u6574\u6279\u53e6\u8bbe\u8f93\u51fa\u3001\u5de5\u4f5c\u3001trace \u548c\u62a5\u544a\u8def\u5f84\u3002\u5148\u6838\u5bf9\u9879\u76ee\u7684 100 \u4e2a run\uff0c\u518d\u6bd4\u8f83\u5404\u5206\u7bb1\u5668\u548c\u6574\u5408\u540e\u7684\u6570\u91cf\u3002\u771f\u5b9e\u961f\u5217\u53ef\u5148\u53d6\u51e0\u4efd\u6709\u4ee3\u8868\u6027\u7684\u6df1\u6d45\u6837\u672c\uff0c\u8fb9\u8dd1\u8fb9\u8bb0\u5f55\u5de5\u4f5c\u76d8\u5360\u7528\uff0c\u5c24\u5176\u7559\u610f\u591a\u4efb\u52a1\u5e76\u53d1\u65f6\u7684\u5cf0\u503c\u3002SRA \u539f\u59cb\u9879\u76ee<\/a><\/p>\n
    \u4ec0\u4e48\u65f6\u5019\u503c\u5f97\u6362\u4e00\u53f0\u670d\u52a1\u5668<\/h2>\n
    \u5982\u679c\u53ea\u60f3\u9a8c\u8bc1\u56fe 2\uff0c\u7528\u524d\u9762\u7684 Python \u811a\u672c\u5373\u53ef\u3002\u771f\u6b63\u6d88\u8017\u7b97\u529b\u7684\u662f\u4ece FASTQ \u91cd\u505a\u7ec4\u88c5\u3001\u8fd0\u884c\u591a\u4e2a\u5206\u7bb1\u5668\u5e76\u4fdd\u7559\u4e2d\u95f4\u6587\u4ef6\u3002\u8bba\u6587\u7684\u57fa\u51c6\u8282\u70b9\u6709\u4e24\u9897 32 \u6838 CPU\u30011 TB \u5185\u5b58\u548c 3 TB SSD\u3002TOFU-MAaPO \u7528\u4e86 110.08 \u5c0f\u65f6\uff0c\u542b\u4e0b\u8f7d\u3002metaFun\u3001ATLAS\u3001nf-core\/mag \u5206\u522b\u4e3a 74.43\u300192.12\u3001430.15 \u5c0f\u65f6\uff0c\u4e09\u8005\u8ba1\u65f6\u5747\u4ece\u9884\u4e0b\u8f7d\u4e4b\u540e\u5f00\u59cb\u3002\u5206\u7bb1\u5668\u7ec4\u5408\u548c\u6267\u884c\u8bbe\u7f6e\u4e5f\u6709\u5dee\u5f02\uff0c\u5355\u770b\u603b\u7528\u65f6\u65e0\u6cd5\u5224\u65ad\u6362\u4e00\u4e2a\u6d41\u7a0b\u80fd\u7ed9\u81ea\u5df1\u7684\u961f\u5217\u7701\u51e0\u5929\u3002\u8bba\u6587\u786c\u4ef6\u4e0e\u8ba1\u65f6\u8bf4\u660e<\/a><\/p>\n
    \u82e5\u4f60\u5df2\u7ecf\u51c6\u5907\u6309\u6574\u6279\u6837\u672c\u8dd1\uff0c\u624b\u8fb9\u8282\u70b9\u5374\u7ecf\u5e38\u6392\u961f\u3001\u5185\u5b58\u4e0d\u8db3\u6216\u5de5\u4f5c\u76d8\u5403\u7d27\uff0c\u53ef\u4ee5\u5e26\u7740\u6837\u672c\u6570\u3001\u538b\u7f29 FASTQ \u603b\u91cf\u3001\u9884\u8ba1\u4fdd\u7559\u54ea\u4e9b\u4e2d\u95f4\u6587\u4ef6\uff0c\u4ee5\u53ca\u8bd5\u8dd1\u7684 trace<\/strong>\uff0c\u548c\u4e91\u751f\u4fe1\u6838\u5bf9\u53ef\u79df\u8282\u70b9\u7684\u5185\u5b58\u3001\u4e34\u65f6\u76d8\u4e0e\u5e76\u53d1\u6570\u3002\u82e5\u5361\u5728\u67d0\u4e00\u4e2a\u5206\u7bb1\u4efb\u52a1\uff0c\u9644\u4e0a\u8be5\u4efb\u52a1\u7684\u5cf0\u503c\u548c\u9519\u8bef\u65e5\u5fd7\uff0c\u6bd4\u62a5\u4e00\u4e2a\u671f\u671b\u6838\u6570\u66f4\u5bb9\u6613\u4f30\u51c6\u8d44\u6e90\u3002\u4e91\u751f\u4fe1\u751f\u4fe1\u670d\u52a1\u5668\u79df\u8d41<\/a><\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"
    \u6253\u5f00 ATLAS \u7684\u9010 bin \u8bc4\u5206\u8868\uff0c\u6838\u5bf9 TOFU-MAaPO \u8bba\u6587\u56fe 2 \u4e2d\u56db\u4e2a\u6d41\u7a0b\u7684\u6570\u91cf\uff0c\u89e3\u91ca\u8d28\u91cf\u95e8\u69db\uff0c\u5e76\u4ece\u4e00\u4e2a\u539f\u59cb\u6837\u672c\u8bbe\u8ba1\u7ec4\u88c5\u8bd5\u8dd1\u3002\u542b Python \u811a\u672c\u3002<\/p>\n","protected":false},"author":1,"featured_media":67113,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_feature_clip_id":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_post_was_ever_published":false},"categories":[1,75],"tags":[385,451,621,383,618],"class_list":["post-67112","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-part","category-compute-environment","tag-mag","tag-nextflow","tag-tofu-maapo","tag-383","tag-618"],"jetpack_sharing_enabled":true,"jetpack_featured_media_url":"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2026\/11\/fig2-reproduction.png?fit=1080%2C800&ssl=1","_links":{"self":[{"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/posts\/67112","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/comments?post=67112"}],"version-history":[{"count":2,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/posts\/67112\/revisions"}],"predecessor-version":[{"id":67211,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/posts\/67112\/revisions\/67211"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/media\/67113"}],"wp:attachment":[{"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/media?parent=67112"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/categories?post=67112"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/tags?post=67112"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}