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Many .sra files are compressed against a reference which is not included in the .sra file.
The SRA-tools prefetch or fastq-dump automatically download both the .sra files and the reference sequences required for decompressing. Additionally it gives download success control.
→ Download SRA-files using prefetch
Download using wget
(not recommended)
# get SRA file location on NCBI server (alternatively, search at NCBI website)
srapath SRR649944
http://sra-download.ncbi.nlm.nih.gov/srapub/SRR649944
# download using wget
wget -P Data http://sra-download.ncbi.nlm.nih.gov/srapub/SRR649944
ls Data/
SRR649944
# converting SRA file into fastq
fastq-dump --split-3 Data/SRR649944
ls
SRR649944_1.fastq
SRR649944_2.fastq
Error
many samples will not work using wget, as the compression related reference genome is missing
Error: "name not found while resolving tree within virtual file system module - failed"
Solution: use prefetch or fastq-dump, instead of wget
Note:
fastq-dump --split-3 SRR649944 (only access number without path Data/SRR649944 or ./SRR649944) will force fastq-dump to download the sample directly from NCBI instead of using the local copy.