Common Questions: SRA Toolkit
May 18 2017
A common question
I was downloading SRA files and convert them into fastq files in gz format. However, I got an error message (pasted below). I noticed that
“Disk quota exceeded” was mentioned. Not sure why I received such error.
How do deal with this issue
When using the SRA, the ncbi uses home as a temp directory while downloading reads. This will COMPLETELY blow through your home space (which is only 100GB)! Here's how to avoid this while using SRA tools:
1) Go to your home directory, and see if there is a hidden folder called .ncbi:
ls -lah ~ #should list .ncbi as a folder! (the -a makes all folders starting with a . appear)
2) Change the directory ncbi uses as temporary space:
echo '/repository/user/main/public/root = "/N/dc2/scratch/USERNAME/ncbi"' > /N/u/USERNAM/Mason/.ncbi/user-settings.mkfg
NOTE: This is an example - you can set that location anywhere you'd like. I recommend in your scratch space! Also, make sure you uses single quotes around the whole echo command and double quotes around your path!
3) Check to make sure the location has changed:
module load sra-toolkit
This will bring up a blue interface - look at the bottom right corner. It should say the path you just gave it! Hit 7 to quit.
That should fix the problem! The temporary files should go to scratch, or wherever else you directed it, and not use the whole home quota. Do note that it is a good idea to check that directory occasionally and delete the .ncbi or ncbi directory you created - it still takes up a lot of space for files you aren’t using!