SRA原始数据下载-aspera-ascp命令Mortix

一、前置环境

win11子系统Ubuntu 20.0

安装aspera-cli (aspera的升级版)

conda install -c hcc aspera-cli

安装后需要找到asperaweb_id_dsa.openssh

 /home/yang/miniconda3/pkgs/aspera-cli-3.9.6-h5e1937b_0/etc/asperaweb_id_dsa.openssh

二、数据下载

2.1 利用ascp下载

下载SRR_list

NCBI-All Databases 输入PRJN或SRP或SRR号

如人SRP048601

点击SRA

 点击 Send results to Run selector

 勾选需要的个体或全选，然后点击Accession List，其中Metadata下载的是完整信息列表

SRR+6位、7位或8位数均可用以下代码

ascp下载代码

echo SRA_datadown
openssh=/home/yang/asperaweb_id_dsa.openssh
cat SRR_list |while read id
donum=`echo $id | wc -m `if [ $num -eq 12 ]then	dateecho "SRR + 8"x=$(echo $id | cut -b 1-6)y=$(echo $id | cut -b 10-11)echo "Downloading $id "(ascp -QT -l 300m -P 33001 -k 1 -i $openssh era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/$x/0$y/$id/   ./)elif  [ $num -eq 11 ]then	dateecho  "SRR + 7"x=$(echo $id | cut -b 1-6)y=$(echo $id | cut -b 10-10)echo "Downloading $id "( ascp  -QT -l 500m -P33001  -k 1 -i $openssh  era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/$x/00$y/$id/   ./)elif [ $num -eq 10 ]thendateecho  "SRR + 6"x=$(echo $id |cut -b 1-6)echo "Downloading $id "( ascp  -QT -l 500m -P33001 -k 1 -i  $openssh era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/$x/$id/   ./ )fi
done

注意：SRR_list行尾应有$

具体可用cat -E file查看

有^M的可通过dos2unix file 去除

此外，由于ascp部分数据下载不全，需设定定时重启该脚本以确定每一个数据的完整性(断点续传

-k 1)

2.2 Mortix

ascp有时因服务器维护不可用，直接使用Mortix下载ftp,容易中断需手动恢复，或者使用Linux的wget 断点下载

先在ENA 中搜索PRJN或SRP或SRR

右击获取连接

或者直接利用代码批量生成ftp链接

echo SRA_datadown
openssh=/home/yang/asperaweb_id_dsa.openssh
cat SRR_list |while read id
donum=`echo $id | wc -m `if [ $num -eq 12 ]then	dateecho "SRR + 8"x=$(echo $id | cut -b 1-6)y=$(echo $id | cut -b 10-11)echo "Downloading $id "echo ftp://ftp.sra.ebi.ac.uk/vol1/fastq/$x/0$y/$id/{id}_1.fastq.gzecho ftp://ftp.sra.ebi.ac.uk/vol1/fastq/$x/0$y/$id/{id}_2.fastq.gzelif  [ $num -eq 11 ]then	dateecho  "SRR + 7"x=$(echo $id | cut -b 1-6)y=$(echo $id | cut -b 10-10)echo "Downloading $id "echo ftp://ftp.sra.ebi.ac.uk/vol1/fastq/$x/00$y/$id/{id}_1.fastq.gzecho ftp://ftp.sra.ebi.ac.uk/vol1/fastq/$x/00$y/$id/{id}_2.fastq.gzelif [ $num -eq 10 ]thendateecho  "SRR + 6"x=$(echo $id |cut -b 1-6)echo "Downloading $id "echo ftp://ftp.sra.ebi.ac.uk/vol1/fastq/$x/$id/{id}_1.fastq.gzecho ftp://ftp.sra.ebi.ac.uk/vol1/fastq/$x/$id/{id}_2.fastq.gzfi
done

 参考

Aspera——利用SRR号批量高效下载FASTQ或SRA数据 - 知乎 (zhihu.com)

在Linux中如何去除文档里^M？_E.die的博客-CSDN博客_文档去除m