fasterq-dump error: about grabseqs HOT 3 CLOSED

Hi Raphael, I'm glad it's been useful (and that it works for someone outside our lab)! I haven't seen that particular error before, but I have a few thoughts for things you might try.

Caching is always a good guess--NCBI loves to cache the SRA data, and caching is on by default (and the cache is basically all of your sequences, which is not ideal). Have you turned it off using vdb-config -i as in the grabseqs readme? See this link for more info. If you did have caching turned on, I'd recommend removing the directory made by sra-toolkit...usually it's located at ~/ncbi. My guess is that maybe this is the cause of the running-out-of-space error? I managed to download that particular SRR without error, so if that doesn't work please let me know and I'm happy to help debug further.

from grabseqs.

Hi Louie,

Thanks for the quick feedback.

I've had look, and the ~/ncbi folder is by default on a low space disk that was full ($HOME). I've turned it off as suggested and it's working fine!

Cheers,
Raphael

from grabseqs.

Sweet, I'm glad it worked!

from grabseqs.