用Aspera connect从NCBI上下载SRA格式数据
2016-01-13 22:08
585 查看
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:$PATH
4.
三 prefetch直接调用ascp,没有安装ascp之前直接用httpprefetch -v DRR047094
hadoop@Mcnode1:~/.aspera/connect/bin$ 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/
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httpprefetch -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/
相关文章推荐
- 08 中国可能再遭基因武器(非典变异)袭击
- 解读英特尔高性能基因
- 数据处理——两文件快速对接
- 使用速铂Aspera下载NGS数据
- 时尚的基因是创新 -- 旺旺平台产品线员工大会即兴发言提要
- 刘强东“价值论”的不死基因
- 一颗基因药能让猩猩说话吗?
- 阻止疟疾传播 科学家用基因改造使蚊子无法飞行
- 天赋是牛人的基因?
- lincRNA和microRNA
- 基于基因组数据的癌症亚型发现聚类研究
- 生物知识学习记录
- 预言实现不远了
- 美国基因检测公司 Veritas Genetics 客户数据遭泄露
- casperJs的安装2
- 禁止通过网页URL访问文件夹 asp.net
- 禁止通过网页URL访问文件夹 asp.net
- 比较分析 Spring AOP 和 AspectJ 之间的差别
- 无法激活服务,因为它不支持 ASP.NET 兼容性
- 在asp.net handler 中 使用 session