classify_wf:基于GTDB参考树,基因组物种注释,包括鉴定、比对、分类三步 de_novo_wf:推荐新树并用GTDB注释,包括鉴定、比对、推断树、确定根和装饰 主要方法模块: identify:基因组中鉴定标记基因 align:多序列对齐 classify:确定物种分类 infer:从多序列对齐序列建树 root:使用外类群定根 decorate:使用GTDB分类注释树 ...
github点击跳转 gtdbtk classify_wf --genome_dir ./data --out_dir./result--extension .fna --cpus 18MESSAGE: [Errno 2] No such file or directory: '/home/wentao/miniconda3/envs/gtdbtk/share/gtdbtk-1.7.0/db/markers/pfam/individual_hmms/PF01868.17.hmm 使用iqtree构建进化树 使用conda安装,这个...
github点击跳转 gtdbtk classify_wf --genome_dir ./data --out_dir./result--extension .fna --cpus 18 MESSAGE: [Errno 2] No such file or directory: '/home/wentao/miniconda3/envs/gtdbtk/share/gtdbtk-1.7.0/db/markers/pfam/...
Additional navigation options master 13Branches46Tags Code Folders and files Name Last commit message Last commit date Latest commit pchaumeil Update classify_wf.ipynb Mar 5, 2025 0f1ae4e·Mar 5, 2025 History 964 Commits .github refactor(config): Refactored config to read variables dependent on ...
classify_wf_options.recalculate_red = False self.optionparser.align(classify_wf_options) self.optionparser.classify(classify_wf_options) summary_out = os.path.join(classify_wf_options.out_dir, PATH_AR122_SUMMARY_OUT.format(prefix=classify_wf_options.prefix)) summary_out = os.path.join(classify...
usage: gtdbtk classify_wf (--genome_dir GENOME_DIR | --batchfile BATCHFILE) --out_dir OUT_DIR [-x EXTENSION] [--min_perc_aa MIN_PERC_AA] [--prefix PREFIX] [--cpus CPUS] [--force] [--scratch_dir SCRATCH_DIR] [-r] [-d] [-h] ...
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> gtdbtk classify_wf --cpus 24 --genome_dir ./my_genomes --out_dir gtdbtk_output The taxonomic classification of each bacterial and archaeal genome is contained in the <prefix>.bac120.summary.tsv and <prefix>.ar122.summary.tsv output files....
gtdbtk classify_wf --genome_dir ./data --out_dir./result--extension .fna --cpus 18 MESSAGE: [Errno 2] No such file or directory: '/home/wentao/miniconda3/envs/gtdbtk/share/gtdbtk-1.7.0/db/markers/pfam/individual_hmms/PF01868.17.hmm ...
gtdbtk classify_wf --genome_dir ./data --out_dir./result--extension .fna --cpus 18MESSAGE: [Errno 2] No such file or directory: '/home/wentao/miniconda3/envs/gtdbtk/share/gtdbtk-1.7.0/db/markers/pfam/individual_hmms/PF01868.17.hmm ...