fastq-dump error: transfer unknown

Question

[mufernando]

Hi, everyone,

I've been trying to download fastq files from SRA. For that, I run the following command:

fastq-dump "$i" --split-files 2> log/fastq-dump.log

As the files are very large, I leave it running and then check the STDERR in which an error is returned:

2016-06-24T00:45:52 fastq-dump.2.6.2 err: transfer unknown while writing log within application support module - SRASplitter_Release

The files are downloaded, but I'm afraid I got only part of it.

Can anybody help me out?

Thanks!

[igor]

I find it easier to wget the SRA files first before converting to FASTQ with fastq-dump.

Also, check ENA where the same files are already in FASTQ format: http://www.ebi.ac.uk/ena

[ablanchetcohen]

Same here. Good old wget works better than all the other solutions proposed by EBI.

[GenoMax]

Did you mean to say NCBI?

[ablanchetcohen]

Right. Sorry. I meant NCBI.

[microfuge]

On a tangent here by I usually like to add a --gzip to fastq-dump . In case something happened to download the decompression will reveal a problem.