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5.1 years ago
Lina F ▴ 200

Hi all,

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



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?

~Lina

UPDATE:

The files were indeed in \$HOME/ncbi/public/sra.

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!

sra prefetch toolkit • 6.0k views
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They probably went into this folder structure sra/sra/SRR2062521

Edit: Did you ever run vdb-config -i (you would need X11 for this) command? If you did then you would have selected a directory to hold the SRA data. I am not sure if this is requirement but the path above is relative to the directory I had selected when I ran vdb-config.

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I never ran vdb-config -i but I found the files in the ncbi/public/sra folder.

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Running that command will allow you to assign a different directory to hold the downloaded files in case you have any restrictions on your local/home directory.

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5.1 years ago
Tonor ▴ 470

Do you have an ncbi/public/sra folder in your home directory - that is where my .sra files end up - but it was so long ago I installed it I'm not sure if its the default location

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Thanks for the info -- that folder does exist and is full of SRA files :D

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yes this folder exist