Question

Failed to set session genome to ...

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federico.comoglio ▴ 100

@federicocomoglio-4524

Last seen 7.4 years ago

Switzerland

Hi All,

I just downloaded the latest GenomicFeatures, and noticed that although the Drosophila dm6 genome is within the output returned by ucscGenomes(), neither refGene, ensGene or flyBaseGene tables can be retrieved using:

txdb <- makeTxDbFromUCSC( "dm6", tablename = "ensGene" )
Error in `genome<-`(`*tmp*`, value = "dm6") :
  Failed to set session genome to 'dm6'

Am I missing something? A quick look into the source indicates that the error is raised from setReplaceMethod("genome","UCSCSession",...)

Thanks a lot for your help.

Federico

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.0 (Maipo)

locale:
[1] LC_CTYPE=C                LC_NUMERIC=C
[3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
[5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8       LC_NAME=C
[9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] BSgenome.Dmelanogaster.UCSC.dm6_1.4.1 BSgenome_1.36.0
[3] rtracklayer_1.28.2                    BiocInstaller_1.18.1
[5] GenomicFeatures_1.20.0                AnnotationDbi_1.30.1
[7] Biobase_2.28.0                        VariantAnnotation_1.14.1
[9] Rsamtools_1.20.1                      Biostrings_2.36.0
[11] XVector_0.8.0                         GenomicRanges_1.20.3
[13] GenomeInfoDb_1.4.0                    IRanges_2.2.1
[15] S4Vectors_0.6.0                       BiocGenerics_0.14.0

loaded via a namespace (and not attached):
[1] zlibbioc_1.14.0         GenomicAlignments_1.4.1 BiocParallel_1.2.1
[4] tools_3.2.0             DBI_0.3.1               lambda.r_1.1.7
[7] futile.logger_1.4.1     futile.options_1.0.0    bitops_1.0-6
[10] RCurl_1.95-4.6          biomaRt_2.24.0          RSQLite_1.0.0
[13] XML_3.98-1.

genomicfeatures makeTxDbFromUCSC • 3.2k views

ADD COMMENT • link updated 9.2 years ago by Michael Lawrence ★ 11k • written 9.6 years ago by federico.comoglio ▴ 100

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I also tried to supply a different genome argument (e.g. hg19, mm9 or dm3) and I get the same error.

ADD REPLY • link 9.6 years ago federico.comoglio ▴ 100

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Hi Federico,

Not sure what's going on but note that there is no ensGene or flyBaseGene table for dm6. Using the refGene table works for me:

txdb <- makeTxDbFromUCSC( "dm6", tablename="refGene" )
txdb
# TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: UCSC
# Genome: dm6
# Organism: Drosophila melanogaster
# UCSC Table: refGene
# Resource URL: http://genome.ucsc.edu/
# Type of Gene ID: Entrez Gene ID
# Full dataset: yes
# miRBase build ID: NA
# transcript_nrow: 35411
# exon_nrow: 82026
# cds_nrow: 62778
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2015-05-07 10:04:55 -0700 (Thu, 07 May 2015)
# GenomicFeatures version at creation time: 1.20.1
# RSQLite version at creation time: 1.0.0
# DBSCHEMAVERSION: 1.1

FWIW a more direct way to reproduce your problem would be for you to try:

library(rtracklayer)
session <- browserSession()
genome(session) <- "dm6"

Can you confirm? If so, it looks like a network issue to me (proxy, firewall, etc...)

H.

ADD REPLY • link 9.6 years ago Hervé Pagès 16k

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Hi Herve',

thanks for your message. The problem seems to be generalized, though. I get:

> library(rtracklayer)
> session <- browserSession()
> genome(session) <- "dm6"
Error in `genome<-`(`*tmp*`, value = "dm6") :
  Failed to set session genome to 'dm6'

I'm running this code on the server I regularly use for my R/BioC work, which is connected to the internet with unmodified network settings.

> is.character(RCurl::getURL("www.google.com"))
[1] TRUE

Let me know if you have an idea on how to fix this issue. Thanks a lot,

Federico

ADD REPLY • link 9.6 years ago federico.comoglio ▴ 100

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This is just another one of those rtrackalyer issues that varies by internet connection. You could try debugging it on your end, but otherwise, there is nothing that we can really do.

ADD REPLY • link 9.6 years ago Michael Lawrence ★ 11k

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Thank you, Michael.

ADD REPLY • link 9.6 years ago federico.comoglio ▴ 100

score 1 · Answer 1 · 2015-05-08

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federico.comoglio ▴ 100

@federicocomoglio-4524

Last seen 7.4 years ago

Switzerland

Currently, this works:

makeTxDbFromUCSC('dm6', tablename = 'refGene', url = 'http://genome-euro.ucsc.edu/cgi-bin/')

ADD COMMENT • link 9.6 years ago federico.comoglio ▴ 100

score 0 · Answer 2 · 2015-10-26

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Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 3.0 years ago

United States

For the record, anyone still experiencing this issue should update to the latest Bioconductor release.

ADD COMMENT • link 9.2 years ago Michael Lawrence ★ 11k