Trouble downloading files with fasterq-dump

Question

[Rogerio Ribeiro]

Hello Biostars, I've been trying download sequence files from NCBI using fasterq-dump. However, I'm having issues, as some of my sample stop the download when the following error occurs: 2021-04-02T17:01:06 fasterq-dump.2.11.0 err: storage exhausted while writing file within file system module - system bad file descriptor error fd='9'

I queried google for this error and it seems to be a storage issue. However, I should have enough space of my current environment and my home dir did not increase size during the download (I checked using DF every 10 minutes). How can I solve this problem?

Cheers

Answer 1

[GenoMax]

Have you run vdb-config to set a location for temp directory where files are temporarily cached when they are being downloaded. If not you should do that first. Point that location to storage where there is space available (it may currently be set to /tmp or /temp).

See instructions here (configuring SRAToolkit section) but replace paths that are relevant to your system.

[Rogerio Ribeiro]

It worked!