SRA Toolkit - prefetch

SRA Toolkit: prefetch

SRA Toolkit Documentation
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Tool: prefetch

Usage:

prefetch [options]

Frequently Used Options:

General:

-h | –help Displays ALL options, general usage, and version information.
帮助信息
-V | –version Display the version of the program.
版本号

Data transfer:

-f | –force Force object download. One of: no, yes, all. no [default]: Skip download if the object if found and complete; yes: Download it even if it is found and is complete; all: Ignore lock files (stale locks or if it is currently being downloaded: use at your own risk!).
强制下载
默认：文件已经存在则跳过
yes: 即使已存在完整文件仍然下载

–transport Value one of: ascp (only), http (only), both (first try ascp, fallback to http). Default: both.
传输
默认： 先尝试ascp, 再尝试http

-l | –list List the contents of a kart file.
列表kart文件
-s | –list-sizes List the content of kart file with target file sizes.
列表Kart文件及文件大小
-N | –min-size Minimum file size to download in KB (inclusive).
最小下载文件大小
-X | –max-size Maximum file size to download in KB (exclusive). Default: 20G.
最大下载文件大小
默认 20G
-o | –order Kart prefetch order. One of: kart (in kart order), size (by file size: smallest first). default: size.
Kart文件下载顺序
默认：按文件大小顺序下载
-a | –ascp-path

Use examples:

prefetch cart_0.krt
下载krt中列表文件
Download the files listed in the kart file.

prefetch -l cart_0.krt
Lists the contents of the kart file.
列表krt

prefetch -X 200G cart_0.krt
Sets the maximum download file size to 200GB and downloads the files listed in the kart.
最大下载文件大小设置为200G

prefetch -o kart cart_0.krt
Downloads the contents in the order listed in the kart. Preferred for large run sets (example: 100+) where calculating the download sizes may cause a delay to the start of downloads.
按顺序下载
文件太多如果按大小顺序下载会造成下载延迟

prefetch -a “/opt/aspera/bin/ascp|/opt/aspera/etc/asperaweb_id_dsa.openssh” SRR390728

When the toolkit is unable to locate an installed version of Aspera, the location of ascp and ssh key (-a /opt/aspera/bin/ascp|/opt/aspera/bin/asperaweb_id_dsa.openssh”) can be provided.
无法自动调用Aspera时就需要提供ascp的路径和密钥

prefetch -t ascp -a “/opt/aspera/bin/ascp|/opt/aspera/bin/asperaweb_id_dsa.openssh” –option-file file.txt

Will force download to be only through aspera (-t ascp) and will prevent http download, default operation is to attempt ascp first and use http if Aspera is not found or fails. Will sequentially download the SRA data files and references required for a list of accessions in “file.txt”. The format for “file.txt” is a newline-separated list of accessions: SRR# SRR# SRR# …
强制aspera下载
file文件的格式为
SRR##
SRR##
…

prefetch ~/Downloads/SRR390728.sra

If you have already downloaded an SRA datafile (example here: SRR390728.sra, present in the “~/Downloads” directory), this command will retrieve all of the reference sequences required to extract the data. This command is useful for resolving errors of the type “name not found while resolving tree” - meaning that a reference(s) is required, but cannot be located.
SRR文件已经在Downloads路径中,
命令用于检索提取已有数据的参考序列
适用于报错： “name not found while resolving tree”

prefetch -c SRR390728

This command will check the availability of all needed reference sequences (-c) for a given accession.
检查给定序列号是否可以能够下载

Possible errors and their solution:
错误及解决方案
path not found while resolving tree within virtual file system module ‘/SRR*.sra’ cannot be found.”
Check to make sure the file and path you have specified exist on your system, also check the path name for typos.
检查路径名

param invalid while parsing argument list - ascp-path expected in the following format: –ascp-path “