Question: Slow Download From TCGA
1
gravatar for dirigible2012
4.8 years ago by
dirigible2012310
European Union
dirigible2012310 wrote:

Is anybody else having problems with a slow download of files from TCGA? At the moment it's taking me 1 hour to download 1 Gb of data using the File Search. My downloads of files from other sources run at about 5MB/second.

Is there anything I can do about this?

Thanks,

Stephanie

tcga • 1.7k views
ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by dirigible2012310

Suddenly, Biostars feels like a homey bioinformatics lab, where everyone pings each other over IM when the cluster disks are being slow. :)

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by Cyriac Kandoth5.3k
2
gravatar for Cyriac Kandoth
4.8 years ago by
Cyriac Kandoth5.3k
Memorial Sloan Kettering, New York, USA
Cyriac Kandoth5.3k wrote:

I'm getting decent speeds of 4.7 to 5 MB/s, or roughly 40 Mb/s, from the TCGA DCC housed in Bethesda MD, while I'm located relatively nearby in New York. Instead of using File Search, have you tried downloading data directly from the public https share? For example, to download the clinical data matrix for TCGA BRCA, you could do something like:

curl -LO https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/luad/bcr/biotab/clin/nationwidechildrens.org_clinical_patient_luad.txt

If you have credentials to access data in the protected https share, then you can use wget with --user specified, and --ask-password so that it prompts you for one.

ADD COMMENTlink written 4.8 years ago by Cyriac Kandoth5.3k
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