To separate download (prefetch) and conversion tasks (fasterq-dump).

Example

1) prefetch: download only raw SRA files

Example: download NCBI-SRA sequence data file SRR649944 into SRA_download/ directory

( Older prefetch versions stored SRA files in $HOME/ncbi/public/sra/ )

prefetch SRR649944 -O SRA_download/

ls SRA_download/*/*

SRR649944/SRR649944.sra

2) fasterq-dump: convert SRA to FASTQ

The locally stored SRA files can be converted by fasterq-dump into .fastq files, saved in directory FASTQ_files/

Additionally using gzip to compress .fastq files

fasterq-dump --split-3 SRA_download/SRR649944 -O FASTQ_files/

gzip FASTQ_files/*.fastq

ls FASTQ_files/

SRR649944_1.fastq.gz

SRR649944_2.fastq.gz


# Note, addressing the SRA identifier without exact path may cause re-download

fasterq-dump --split-3 SRR649944

If the SRA file is not located in the current working directory, fasterq-dump will download the file again using the default temporary directory $TMPDIR if no other download location is pre-defined as CACHE in → SRA-toolkit configuration.

ls $TMPDIR/.nfs*

/tmp/.nfs00000000558ac9cf

Options

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

prefetch --max-size 100G SRR649944


Read more

https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump

prefetch --help