I would like to download a few datasets from NCBI's SRA resource. I installed the SRA toolkit on a Mac (10.11.6) and tried to download a run as follows:
lina$ ./prefetch Usage: 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 lina$ ./prefetch SRR2062521 2016-10-26T17:49:13 prefetch.2.8.0: 1) Downloading 'SRR2062521'... 2016-10-26T17:49:13 prefetch.2.8.0: Downloading via http... 2016-10-26T18:02:20 prefetch.2.8.0: 1) 'SRR2062521' was downloaded successfully
Unfortunately, I don't know where the downloaded files went. I can't find them in the current working directory, and I also can't find them through the search box.
Do I need to pipe the output somewhere?
Thanks for any advice!
The files were indeed in
I also found that this command worked to download the files to the current working directory:
fastq-dump –origfmt –split-3 SRR001666
Thanks for all the help!