Question: Cannot find downloaded files from SRA toolkit (prefetch)
gravatar for Lina F
4.1 years ago by
Lina F200
Boston, MA
Lina F200 wrote:

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
  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 $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!

prefetch toolkit sra • 4.7k views
ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Lina F200

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.

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by GenoMax92k

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

ADD REPLYlink written 4.1 years ago by Lina F200

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.

ADD REPLYlink written 4.1 years ago by GenoMax92k
gravatar for Tonor
4.1 years ago by
Tonor430 wrote:

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

ADD COMMENTlink written 4.1 years ago by Tonor430

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

ADD REPLYlink written 4.1 years ago by Lina F200

yes this folder exist

ADD REPLYlink written 3.0 years ago by prasoonagar10
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