makeTxDbFromBiomart error while building metadata dataframe
0
0
Entering edit mode
@floriandeckert-13733
Last seen 3.5 years ago

Hi, 

I get the following error when trying to build a TxDb object from Biomart. In the forum it is suggseted to build the a TxDb from a gft file. Anyway, I think that command should work and would apreachiate if you might help me to understand what is going wrong. 

Thank you very much!!!

> Ensembl_annoTxDb=makeTxDbFromBiomart(biomart="ensembl",

+                                      dataset="mmusculus_gene_ensembl",
+                                      transcript_ids=NULL,
+                                      circ_seqs=DEFAULT_CIRC_SEQS,
+                                      filter=NULL,
+                                      id_prefix="ensembl_",
+                                      host="www.ensembl.org",
+                                      port=80,
+                                      taxonomyId=NA,
+                                      miRBaseBuild=NA)
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... FAILED! (=> skipped)
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... Error in function (type, msg, asError = TRUE)  : 
  Recv failure: Connection was reset

 

maketxdbfrombiomart • 586 views
ADD COMMENT
0
Entering edit mode

This seems to work for me.

makeTxDbFromBiomart(biomart="ensembl", dataset="mmusculus_gene_ensembl",
                    transcript_ids=NULL, circ_seqs=DEFAULT_CIRC_SEQS,
                    filter=NULL, id_prefix="ensembl_",
                    host="www.ensembl.org", port=80,
                    taxonomyId=NA, miRBaseBuild=NA)
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Mus musculus
# Taxonomy ID: 10090
# Resource URL: www.ensembl.org:80
# BioMart database: ENSEMBL_MART_ENSEMBL
# BioMart database version: Ensembl Genes 90
# BioMart dataset: mmusculus_gene_ensembl
# BioMart dataset description: mmusculus_gene_ensembl
# BioMart dataset version: GRCm38.p5
# Full dataset: yes
# miRBase build ID: NA
# transcript_nrow: 132305
# exon_nrow: 500562
# cds_nrow: 241239
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2017-09-18 13:01:35 +0200 (Mon, 18 Sep 2017)
# GenomicFeatures version at creation time: 1.29.9
# RSQLite version at creation time: 2.0
# DBSCHEMAVERSION: 1.1

Can you include the output of the command sessionInfo(), so we can see what versions of packages you're using.  Here's mine for comparison.

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 18.1

Matrix products: default
BLAS: /home/msmith/Applications/R/R-3.4.1/lib/libRblas.so
LAPACK: /home/msmith/Applications/R/R-3.4.1/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] GenomicFeatures_1.29.9 AnnotationDbi_1.39.3   Biobase_2.37.2        
[4] GenomicRanges_1.29.14  GenomeInfoDb_1.13.4    IRanges_2.11.16       
[7] S4Vectors_0.15.8       BiocGenerics_0.23.1   

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12               compiler_3.4.1            
 [3] XVector_0.17.1             prettyunits_1.0.2         
 [5] bitops_1.0-6               tools_3.4.1               
 [7] zlibbioc_1.23.0            progress_1.1.2            
 [9] biomaRt_2.33.5             digest_0.6.12             
[11] bit_1.1-12                 lattice_0.20-35           
[13] RSQLite_2.0                memoise_1.1.0             
[15] tibble_1.3.4               rlang_0.1.2               
[17] Matrix_1.2-11              DelayedArray_0.3.19       
[19] DBI_0.7                    GenomeInfoDbData_0.99.1   
[21] rtracklayer_1.37.3         stringr_1.2.0             
[23] Biostrings_2.45.4          grid_3.4.1                
[25] bit64_0.9-7                R6_2.2.2                  
[27] XML_3.98-1.9               BiocParallel_1.11.8       
[29] blob_1.1.0                 magrittr_1.5              
[31] matrixStats_0.52.2         Rsamtools_1.29.1          
[33] GenomicAlignments_1.13.6   assertthat_0.2.0          
[35] SummarizedExperiment_1.7.8 stringi_1.1.5             
[37] RCurl_1.95-4.8      

 

ADD REPLY

Login before adding your answer.

Traffic: 185 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6