Download SRA sequence read sample files from NCBI

prefetch Sequence-run-ID

downloads and stores .sra files in



prefetch SRR649944

ls ~/ncbi/public/sra/


The locally stored .sra file can be accessed by fastq-dump for further processing

fastq-dump --split-3 SRR649944



If the .sra file is not located in $HOME/ncbi/public/sra/ fastq-dump will download again.


# set maximum file size download limit to 100G (default: 20G)

prefetch --max-size 100G SRR649944

read more

prefetch --help


prefetch [options] <SRA accession | kart file> [...]

Download SRA or dbGaP files and their dependencies

prefetch [options] <SRA file> [...]

Check SRA file for missed dependencies and download them

prefetch --list <kart file> [...]

List the content of a kart file


-f|--force <value> 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 it is

beeing downloaded by another process: use

at your own risk!)

-t|--transport <value> transport: one of: ascp; http; both. (ascp

only; http only; first try ascp, use http

if cannot download by ascp). Default: both

-l|--list list the content of kart file

-n|--numbered-list list the content of kart file with kart

row numbers

-s|--list-sizes list the content of kart file with target

file sizes

-R|--rows <rows> kart rows (default all). row list should be


-N|--min-size <size> minimum file size to download in KB


-X|--max-size <size> maximum file size to download in KB

(exclusive). Default: 20G

-o|--order <value> kart prefetch order: one of: kart, size. (in

kart order, by file size: smallest first),

default: size

-a|--ascp-path <ascp-binary|private-key-file> path to ascp program and

private key file (asperaweb_id_dsa.putty)

-p|--progress <value> time period in minutes to display download

progress (0: no progress), default: 1

-c|--check-all double-check all refseqs

-h|--help Output brief explanation for the program.

-V|--version Display the version of the program then


-L|--log-level <level> Logging level as number or enum string. One

of (fatal|sys|int|err|warn|info) or (0-5)

Current/default is warn

-v|--verbose Increase the verbosity of the program

status messages. Use multiple times for more

verbosity. Negates quiet.

-q|--quiet Turn off all status messages for the

program. Negated by verbose.

--option-file <file> Read more options and parameters from the


prefetch : 2.3.4