[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?
Thanks,
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?
.
.Thx
.
.Malcolm
.
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