fasterq-dump quit with error code 3

Question

[Maliha]

I am trying to split a paired-end SRA file with this command

fasterq-dump '/home/maliha/asil/SRR10161541'

However, every time I am getting this error message "fasterq-dump quit with error code 3". I am adding the error code message for reference.

[ATpoint]

Is this the correct syntax? I am wondering as I have not used it in a while, but shouldn't it be either like:

# If the SRA file was downloaded via prefetch
fasterq-dump path/to/file.sra

# If you want to pull fastq from the web right away
fasterq-dump <accession> --outdir a_directory --outfile a_outfile.fastq

Answer 1

[Pierre Lindenbaum]

https://github.com/ncbi/sra-tools/issues/171

Typically this error happens when you exhaust the storage set aside for your SRA workspace. Oftentimes, users are unaware that we are using a workspace to cache downloaded data, and by default this is in your $HOME directory, although it almost never is the best place (it's the only one we can set as default, though!).

PS: why a screenshot when you can just copy-n-paste the text ?

[Maliha]

Thanks for answering. I think now I have to search if I can add any temporary space. I used to copy paste the error message. But in my other posts someone mentioned that I should give picture of the error message so that people can understand it better.

[GenoMax]

You can to run vdb-config to set locations for temp space. Do that if you have not done so.

[gernophil]

Is rthere a way to set the cache directory, if you’re using the snakemake wrapper?