[Bioc-devel] SRAdb listSRAfile returns empty datatable with filetype='fastq'

Cook, Malcolm MEC at stowers.org
Thu Feb 14 00:23:37 CET 2013

H'lo datasubs,

I have been using the BioConductor R package called SRAdb, supported by Jack Zhu, cc:ed, which provides programmatic access to your ftp archive of SRA submissions.

It stopped working a few minutes ago, and after sleuthing, I found this perhaps related announcement on your site: http://www.ebi.ac.uk/ena/about/news#news_127

Am I accessing in an administrative window, or are you possibly discontinuing or modifying you support for SRA fastq archives?


Malcolm Cook

 .-----Original Message-----
 .From: bioc-devel-bounces at r-project.org [mailto:bioc-devel-bounces at r-project.org] On Behalf Of Cook, Malcolm
 .Sent: Wednesday, February 13, 2013 5:18 PM
 .To: 'bioc-devel at r-project.org'; 'zhujack at mail.nih.gov'
 .Subject: [Bioc-devel] SRAdb listSRAfile returns empty datatable with filetype='fastq'
 .Hi Jack,
 .Do you happen to know if EBI is refreshing or otherwise administering their archive of SRA fastqs?

Sluething their site, I suspect this announcement is related:  http://www.ebi.ac.uk/ena/about/news#news_127

 .I find  that if I change the type to 'sra', I get a quick list of paths.  But if go after the 'fastq', the result yesterday, which worked, is
 .coming back empty this afternoon.
 .Any ideas?
 .Bioc-devel at r-project.org mailing list

More information about the Bioc-devel mailing list