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Question: SRAdb listFastq error
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gravatar for Mark Dunning
6.9 years ago by
Mark Dunning1.0k
Cancer Research Uk Cambridge Institute, Cambridge (until October 2017)
Mark Dunning1.0k 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 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
ADD COMMENTlink modified 6.9 years ago by Sean Davis21k • written 6.9 years ago by Mark Dunning1.0k
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gravatar for Sean Davis
6.9 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
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_Stat ic_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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 6.9 years ago by Sean Davis21k
0
gravatar for Sean Davis
6.9 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Wed, Jan 5, 2011 at 7:47 AM, Mark Dunning <mark.dunning@gmail.com> wrote: > Hi Sean, > > That's a shame. Thanks for the information. I think I can get the > fastqs I need by another means though. > > You don't have to work too hard at it. The process is described here: http://www.ncbi.nlm.nih.gov/books/NBK50846/#UsingToolKit_BK.3_Converti ng_SRA_format In short, you'll need the SRA SDK to do so. http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m =software&s=software Binaries are available for several architectures and OSes. Sean > Regards, > > Mark > > On Wed, Jan 5, 2011 at 11:54 AM, Sean Davis <sdavis2@mail.nih.gov> wrote: > > > > > > 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_St atic_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 > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > [[alternative HTML version deleted]]
ADD COMMENTlink written 6.9 years ago by Sean Davis21k
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