用Aspera connect从NCBI上下载SRA格式数据

用Aspera connect从NCBI上下载SRA格式数据:


一. window

1.下载地址:

http://downloads.asperasoft.com/connect2/


2.安装很简单,略


3.下载:

数据下载地址:

http://www.ncbi.nlm.nih.gov/projects/faspftp/1000genomes/




其他地址:

http://www.1000genomes.org/aspera

可参考【3】


二 linux

1.下载:

curl -O http://download.asperasoft.com/download/sw/connect/3.6.1/aspera-connect-3.6.1.110647-linux-64.tar.gz
tar zxf asper-commect-3.6.1.110647-linux.tar.gz


2.安装

sh aspera-connect-2.4.7.37118-linux-64.sh
或者<pre name="code" class="plain">./aspera-connect-3.6.1.110647-linux-64.sh*

 

3.加入path:

hadoop@Mcnode1:~/.aspera/connect/bin$ vi /etc/profile
......
export ascp_home=/home/hadoop/.aspera/connect
export PATH=$HOME/bin:$JAVA_HOME/bin:$JAVA_HOME/jre/bin:$ascp_home/bin:$PATH


 hadoop@Mcnode1:~/.aspera/connect/bin$ source /etc/profile

4.

三  prefetch直接调用ascp,没有安装ascp之前直接用http

prefetch -v DRR047094

hadoop@Mcnode1:~/.aspera/connect/bin$ prefetch -v DRR047094
Maximum file size download limit is 20,971,520KB

2016-01-13T13:24:46 prefetch.2.5.5: Using 'ascp'
2016-01-13T13:24:46 prefetch.2.5.5: Using 'ascp'
2016-01-13T13:24:46 prefetch.2.5.5: Using '/home/hadoop/.aspera/connect/bin/ascp'
2016-01-13T13:25:06 prefetch.2.5.5: 1) Downloading 'DRR047094'...
2016-01-13T13:25:06 prefetch.2.5.5:  Downloading via fasp...
/home/hadoop/.aspera/connect/bin/ascp /home/hadoop/.aspera/connect/bin/ascp -i /home/hadoop/.aspera/connect/etc/asperaweb_id_dsa.openssh -pQTk1 -l 1000m dbtest@sra-download.ncbi.nlm.nih.gov:data/sracloud/srapub/DRR047094 /home/hadoop/cloud/adam/xubo/data/down-sratool/sra/DRR047094.sra.tmp.94178.tmp
2016-01-13T13:25:44 prefetch.2.5.5 err: process failed while waiting process - ascp failed with 1
/home/hadoop/.aspera/connect/bin/ascp /home/hadoop/.aspera/connect/bin/ascp -i /home/hadoop/.aspera/connect/etc/asperaweb_id_dsa.openssh -pQTk1 -l 1000m dbtest@sra-download.ncbi.nlm.nih.gov:data/sracloud/srapub/DRR047094 /home/hadoop/cloud/adam/xubo/data/down-sratool/sra/DRR047094.sra.tmp.94178.tmp
2016-01-13T13:26:15 prefetch.2.5.5 err: process failed while waiting process - ascp failed with 1
2016-01-13T13:26:15 prefetch.2.5.5:  fasp download failed
2016-01-13T13:26:15 prefetch.2.5.5:  Downloading via http...
2016-01-13T13:26:19 prefetch.2.5.5: http://sra-download.ncbi.nlm.nih.gov/srapub/DRR047094 -> /home/hadoop/cloud/adam/xubo/data/down-sratool/sra/DRR047094.sra.tmp.94178.tmp


数据列表下载:

ascp问题

还有list下载

没解决



参考:

【1】 http://www.plob.org/2012/07/31/3013.html

【2】 https://indexofire.gitbooks.io/notebook_of_analyzing_pathogen_ngs_data/content/chapter_1/sra.html

【3】http://boyun.sh.cn/bio/?p=1933

【4】http://www.bbioo.com/lifesciences/40-115994-1.html

【5】http://blog.163.com/lixuenan200806@126/blog/static/36907807201461192615635/

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