On Wed, Jan 5, 2011 at 6:29 AM, Mark Dunning <mark.dunning@gmail.com> wrote:

> Hi,
>
> I am hoping to download some Fastq files from the Short Read Archive
> and am following the vignette for SRAdb. However, I get an error when
> trying the example of using listFastq
>
> >  listFastq("SRA011804", sra_con = sra_con)
> Error in curlPerform(curl = curl, .opts = opts, .encoding = .encoding) :
>  Server denied you to change to the given directory
>
>
Hi, Mark.  Unfortunately, we are going to have to remove fastq access tools
as NCBI has removed the fastq files:

http://www.ncbi.nlm.nih.gov/books/NBK49286/#SRA_Usability_Chang.2_Static_fastq_dumps

We are looking at workarounds for this, but for the time being, the
functionality is broken and will not likely be retained in the same form.

Sean


> I think I have setup the sra_con object correctly
>
> > sra_con
> <SQLiteConnection: DBI CON (2626, 2)>
> >  dbListFields(sra_con, "study")
>  [1] "study_ID"             "study_alias"          "study_accession"
>  [4] "study_title"          "study_type"           "study_abstract"
>  [7] "center_name"          "center_project_name"  "project_id"
> [10] "study_description"    "study_url_link"       "study_entrez_link"
> [13] "study_attribute"      "submission_accession" "sradb_updated"
> >
>
> Cheers,
>
> Mark
>
>
> > sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C
>  [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8
>  [5] LC_MONETARY=C             LC_MESSAGES=en_GB.utf8
>  [7] LC_PAPER=en_GB.utf8       LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] SRAdb_1.4.0   graph_1.28.0  RSQLite_0.9-3 DBI_0.2-5
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.10.0  GEOquery_2.16.3 RCurl_1.4-3     tools_2.12.0
> [5] XML_3.2-0
>
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