对应的数据库文件会自动下载到${MY_CONDA_ENV_PATH}/lib/python3.9/site-packages/metaphlan/metaphlan_databases。(不懂后面的--Bowtie2db参数有什么用,对下载的数据库似乎无影响),在使用前要记得把数据库路径下的mpa_latest文件内容修改为mpa_vOct22_CHOCOPhlAnSGB_202212,不然在使用中还是会报错。
#二、跑metaphlan鉴定 cat/share/home/xiehs/17.meta/data/hmp/metadata.txt|awk'{if (NR > 1) print $1}'|whileread i;doecho"metaphlan --index ~/Software/miniconda3/envs/mpa/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103 --input_type fastq --npro...
$ bowtie2 --sam-no-hd --sam-no-sq --no-unal --very-sensitive -S metagenome.sam -x ${mpa_dir}/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901 -U metagenome.fastq $ metaphlan metagenome.sam --input_type sam -o profiled_metagenome.txt * We can also natively handle paired-end metagenome...
metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.fna /usr/local/lib/python3.7/dist-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901 # after bowtie2-build completes, should have indexed files in your metaphlan_databases directory $ ls file_list.txt mpa_latest mpa...
安装完成后,直接运行metaphlan,软件会自动下载数据库到默认目录,也就是虚拟环境中python包目录envs/mpa/lib/python3.7/site-packages/metaphlan/metaphlan_databases。软件会先下载file_list.txt文件,文件里包含所有数据库下载链接。接着就是下载和构建index。这是第一次运行时的步骤,之后会跳过这步(除非数据库不在了)...