Question: Cannot find downloaded files from SRA toolkit (prefetch)
1
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
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!

~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!

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
4
gravatar for Tonor
4.1 years ago by
Tonor430
UK
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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1881 users visited in the last hour