sratoolkit 2.11.3安装与使用

备注：下载该版本原因是因为使用2.9.2版本的fastq-dump/fasterq-dump出现了以下错误

fasterq-dump --split-3 SRRid -e 7
2021-12-02T12:47:28 fasterq-dump.2.9.2 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed )
2021-12-02T12:50:24 fasterq-dump.2.9.2 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed )

1.sratoolkit 安装包下载

从NCBI上下载对应版本的安装包

wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.11.3/sratoolkit.2.11.3-ubuntu64.tar.gz

2.解压

tar xzvf sratoolkit.2.11.3-ubuntu64.tar.gz

3.添加环境变量到bashrc文件

export PATH=~/Biosoft/sratoolkit.2.11.3-ubuntu64/bin:$PATH

source ~/.bashrc

配置sratoolkit

vdb-config --interactive

4.使用fasterq-dump进行文件转换

fasterq-dump --split-3 SRRid -e 7