This time the following error occurred after roughly 7-hour no-stop running. OPEN NEW CONNECTION ON FILE: hsa-miR-199a- 5p_V_MirBase_FastaFiles.txt **** WRITE 3UTR SEQUENCE TO FILE: hsa-miR-199a- 5p_V_MirBase_FastaFiles.txt **** Error in getBM(attributes = c("hgnc_symbol", "ensembl_gene_id", "refseq_dna", : Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_56: DBI connect('database=ensembl_mart_ 56;host=martdb.ensembl.org;port=5316','anonymous',...) failed: Can't connect to MySQL server on 'martdb.ensembl.org' (110) at /srv/biomart_server/biomart.org/biomart- perl/lib/BioMart/Configuration/DBLocation.pm line 98 > sessioninfo() Error: could not find function "sessioninfo" > infosession() Error: could not find function "infosession" > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] JGR_1.6-7 iplots_1.1-3 JavaGD_0.5-2 rJava_0.6-3 [5] CORNA_1.2 XML_2.5-1 GEOquery_2.8.0 RCurl_0.98-1 [9] bitops_1.0-4.1 biomaRt_2.0.0 Biobase_2.4.1 gdata_2.4.2 [13] microRNA_1.2.0 Rlibstree_0.3-2 Biostrings_2.12.7 IRanges_1.2.3 loaded via a namespace (and not attached): [1] gtools_2.6.1 tutti i telefonini TIM! [[alternative HTML version deleted]]

I think that you have asked this question (a number of times) before. Please see Steffen's answer to you via the link (and please note Sean's requests): http://thread.gmane.org/gmane.science.biology.informatics.conductor/25 759/focus=25778 Within a 7 hour period, there could be a number of things that can occur between your connection to Biomart. Batch queries would be the way forward as per Steffen's comments if you are not already doing this. On Wed, Nov 18, 2009 at 8:38 AM, <mauede@alice.it> wrote: > This time the following error occurred after roughly 7-hour no-stop > running. > > > > OPEN NEW CONNECTION ON FILE: hsa-miR-199a- 5p_V_MirBase_FastaFiles.txt > > **** WRITE 3UTR SEQUENCE TO FILE: > hsa-miR-199a-5p_V_MirBase_FastaFiles.txt **** > Error in getBM(attributes = c("hgnc_symbol", "ensembl_gene_id", > "refseq_dna", : > Query ERROR: caught BioMart::Exception::Database: Could not connect to > mysql database ensembl_mart_56: DBI connect('database=ensembl_mart_56;host= > martdb.ensembl.org;port=5316','anonymous',...) failed: Can't connect to > MySQL server on 'martdb.ensembl.org' (110) at /srv/biomart_server/ > biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98 > > sessioninfo() > Error: could not find function "sessioninfo" > > infosession() > Error: could not find function "infosession" > > sessionInfo() > R version 2.9.0 (2009-04-17) > x86_64-unknown-linux-gnu > > locale: > > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] JGR_1.6-7 iplots_1.1-3 JavaGD_0.5-2 rJava_0.6-3 > [5] CORNA_1.2 XML_2.5-1 GEOquery_2.8.0 RCurl_0.98-1 > [9] bitops_1.0-4.1 biomaRt_2.0.0 Biobase_2.4.1 gdata_2.4.2 > [13] microRNA_1.2.0 Rlibstree_0.3-2 Biostrings_2.12.7 IRanges_1.2.3 > > loaded via a namespace (and not attached): > [1] gtools_2.6.1 > > > tutti i telefonini TIM! > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Hi, On Nov 18, 2009, at 11:38 AM, <mauede at="" alice.it=""> wrote: > This time the following error occurred after roughly 7-hour no-stop > running. You (still) haven't included the code/query you are sending that gets you this error. What kind of query takes 7 hours to process? Anyway, if your query really is running this long, you could try to break up the query to have it return results on subsets of your data at a time (perhaps on a chromosome by chromosome basis). -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact