Question: fastq-dump error: transfer unknown
0
gravatar for mufernando
22 months ago by
mufernando10
Brazil
mufernando10 wrote:

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!

fastq-dump next-gen sra • 724 views
ADD COMMENTlink written 22 months ago by mufernando10
2

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

ADD REPLYlink modified 22 months ago • written 22 months ago by igor6.2k

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

ADD REPLYlink written 22 months ago by ablanchetcohen1.2k

Did you mean to say NCBI?

ADD REPLYlink written 22 months ago by genomax49k

Right. Sorry. I meant NCBI.

ADD REPLYlink written 22 months ago by ablanchetcohen1.2k

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.

ADD REPLYlink written 22 months ago by microfuge900
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