biomaRt:getBM error when query is large
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Shi, Tao ▴ 720
@shi-tao-199
Last seen 7.1 years ago
Hi list, See the sample codes below, where "rs" is a char vector containing ~430000 rs IDs. However, when I ran the query 10000 at a time, it worked. Is there a query limit for biomaRt? Thanks, ...Tao > tmp <- getBM(c("ensembl_gene_stable_id", "refsnp_id", "allele", "chr_name", "chrom_start", "chrom_strand"), + filters = "refsnp", values = rs, mart = mart) Error in postForm(paste(martHost(mart), "?", sep = ""), query = xmlQuery) : Empty reply from server > sessionInfo() R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_1.14.0 RCurl_0.9-3 GO.db_2.2.0 AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4 Biobase_2.0.1 loaded via a namespace (and not attached): [1] XML_1.95-2
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@steffenstatberkeleyedu-2907
Last seen 7.9 years ago
Hi Tao, I haven't hit a limit yet but you might have. 430.000 ids is quite large. Try to split your query in a few batches of e.g. 100.000 or 50.000 long (you should not need to go below this length). I would also put Sys.sleep(1) between each query so you won't get into trouble of sending a subsequent querying the server to fast after an earlier query. I bet: tmp1 <- getBM(c("ensembl_gene_stable_id", "refsnp_id", "allele","chr_name", "chrom_start", "chrom_strand"),filters = "refsnp", values = rs[1:100000], mart = mart) Sys.sleep(1) tmp2 <- getBM(c("ensembl_gene_stable_id", "refsnp_id", "allele","chr_name", "chrom_start", "chrom_strand"),filters = "refsnp", values = rs[100000:200000], mart = mart) Sys.sleep(1) tmp3 <- getBM(c("ensembl_gene_stable_id", "refsnp_id", "allele","chr_name", "chrom_start", "chrom_strand"),filters = "refsnp", values = rs[200000:300000], mart = mart) Sys.sleep(1) tmp4 <- getBM(c("ensembl_gene_stable_id", "refsnp_id", "allele","chr_name", "chrom_start", "chrom_strand"),filters = "refsnp", values = rs[300000:430000], mart = mart) all = rbind(tmp1,tmp2,tmp3,tmp4) Should do it. Cheers, Steffen > Hi list, > > See the sample codes below, where "rs" is a char vector containing ~430000 > rs IDs. However, when I ran the query 10000 at a time, it worked. Is > there a query limit for biomaRt? > > Thanks, > > ...Tao > > > >> tmp <- getBM(c("ensembl_gene_stable_id", "refsnp_id", "allele", >> "chr_name", "chrom_start", "chrom_strand"), > + filters = "refsnp", values = rs, mart = mart) > Error in postForm(paste(martHost(mart), "?", sep = ""), query = xmlQuery) > : > Empty reply from server > >> sessionInfo() > R version 2.7.0 (2008-04-22) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] biomaRt_1.14.0 RCurl_0.9-3 GO.db_2.2.0 > AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4 Biobase_2.0.1 > > loaded via a namespace (and not attached): > [1] XML_1.95-2 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Shi, Tao ▴ 720
@shi-tao-199
Last seen 7.1 years ago
Thanks, Steffen. That was exactly what I did. I was doing 10000 at a time, just to be safe. ...Tao ----- Original Message ---- From: "steffen@stat.Berkeley.EDU" <steffen@stat.berkeley.edu> To: "Shi, Tao" <shidaxia at="" yahoo.com=""> Cc: bioconductor at stat.math.ethz.ch Sent: Friday, August 1, 2008 3:09:40 PM Subject: Re: [BioC] biomaRt:getBM error when query is large Hi Tao, I haven't hit a limit yet but you might have. 430.000 ids is quite large. Try to split your query in a few batches of e.g. 100.000 or 50.000 long (you should not need to go below this length). I would also put Sys.sleep(1) between each query so you won't get into trouble of sending a subsequent querying the server to fast after an earlier query. I bet: tmp1 <- getBM(c("ensembl_gene_stable_id", "refsnp_id", "allele","chr_name", "chrom_start", "chrom_strand"),filters = "refsnp", values = rs[1:100000], mart = mart) Sys.sleep(1) tmp2 <- getBM(c("ensembl_gene_stable_id", "refsnp_id", "allele","chr_name", "chrom_start", "chrom_strand"),filters = "refsnp", values = rs[100000:200000], mart = mart) Sys.sleep(1) tmp3 <- getBM(c("ensembl_gene_stable_id", "refsnp_id", "allele","chr_name", "chrom_start", "chrom_strand"),filters = "refsnp", values = rs[200000:300000], mart = mart) Sys.sleep(1) tmp4 <- getBM(c("ensembl_gene_stable_id", "refsnp_id", "allele","chr_name", "chrom_start", "chrom_strand"),filters = "refsnp", values = rs[300000:430000], mart = mart) all = rbind(tmp1,tmp2,tmp3,tmp4) Should do it. Cheers, Steffen > Hi list, > > See the sample codes below, where "rs" is a char vector containing ~430000 > rs IDs. However, when I ran the query 10000 at a time, it worked. Is > there a query limit for biomaRt? > > Thanks, > > ...Tao > > > >> tmp <- getBM(c("ensembl_gene_stable_id", "refsnp_id", "allele", >> "chr_name", "chrom_start", "chrom_strand"), > + filters = "refsnp", values = rs, mart = mart) > Error in postForm(paste(martHost(mart), "?", sep = ""), query = xmlQuery) > : > Empty reply from server > >> sessionInfo() > R version 2.7.0 (2008-04-22) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] biomaRt_1.14.0 RCurl_0.9-3 GO.db_2.2.0 > AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4 Biobase_2.0.1 > > loaded via a namespace (and not attached): > [1] XML_1.95-2 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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