官网的安装依赖的方法还是有些麻烦,直接用conda安装!避免报错~
下载数据库
mkdir -p /project/shenmy/biosoftware/kofamscan/db
cd /project/shenmy/biosoftware/kofamscan/db
wget ftp://ftp.genome.jp/pub/db/kofam/ko_list.gz
wget ftp://ftp.genome.jp/pub/db/kofam/profiles.tar.gz
gunzip ko_list.gz
tar xvzf profiles.tar.gz
安装环境
conda create -n kofamscan -c bioconda kofamscan
运行
./exec_annotation -h
Usage: exec_annotation [options] <query>
<query> FASTA formatted query sequence file
-o <file> File to output the result [stdout]
-p, --profile <path> Profile HMM database
-k, --ko-list <file> KO information file
--cpu <num> Number of CPU to use [1]
-c, --config <file> Config file
--tmp-dir <dir> Temporary directory [./tmp]
-E, --e-value <e_value> Largest E-value required of the hits
-T, --threshold-scale <scale>
The score thresholds will be multiplied by this value
-f, --format <format> Format of the output [detail]
detail: Detail for each hits (including hits below threshold)
detail-tsv: Tab separeted values for detail format
mapper: KEGG Mapper compatible format
mapper-one-line: Similar to mapper, but all hit KOs are listed in one line
--[no-]report-unannotated Sequence name will be shown even if no KOs are assigned
Default is true when format=mapper or mapper-all,
false when format=detail
--create-alignment Create domain annotation files for each sequence
They will be located in the tmp directory
Incompatible with -r
-r, --reannotate Skip hmmsearch
Incompatible with --create-alignment
--keep-tabular Neither create tabular.txt nor delete K number files
By default, all K number files will be combined into
a tabular.txt and delete them
--keep-output Neither create output.txt nor delete K number files
By default, all K number files will be combined into
a output.txt and delete them
Must be with --create-alignment
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