Cannot find downloaded files from SRA toolkit (prefetch)
1
1
Entering edit mode
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

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!

sra prefetch toolkit • 6.0k views
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY
4
Entering edit mode
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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

yes this folder exist

ADD REPLY

Login before adding your answer.

Traffic: 2133 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6