fastq-dumper

transfer unknown while writing file within file system module - system I/O error

home folder is full, please clean ncbi folder.

https://www.biostars.org/p/173968/

https://edwards.sdsu.edu/research/fastq-dump/

The SRA (Sequence Read Archive) is a public repository of DNA sequence data. When you run sam-dump or fastq-dump from the sratoolkit, it will first actually use prefetch to download a “temporary” .sra file, which it then converts to either sam or fastq format. By default, sratoolkit will download .sra files to a subfolder in your home folder ($HOME/ncbi/public/sra). This is a bad thing because 1) your home folder may have a space quota, and 2) these downloaded files won’t be useful for others in the group, since they’re in your personal space. It’s better to tell sratoolkit to use a shared filesystem. The advertised way to change the default path uses a graphical interface called vdb-config -i, which is not ideal. Luckily, all this GUI does is add a setting to a config file that sratoolkit reads, so we can bypass the GUI completely and edit the config file directly. Here’s how to change your default data storage path:

echo "/repository/user/main/public/root = \"$DATA\"" > $HOME/.ncbi/user-settings.mkfg

Now, the huge .sra files will be stored in our shared, huge filesystem instead of in your home directory.

To move the .sra files to a shared folder, please go to the fastq-dump folder. Under ncbi, modify the 
default.kfg as above.