Search
Question: Help with error produced when using makeTxDbFromBiomart
0
gravatar for pat20
10 days ago by
pat200
pat200 wrote:

Hello. I am having some problems with using the makeTxDbFromBiomart command. I believe all my packages are up to date and have attached session info. I have also tried re-starting my session incase that was the problem. Any help would be much appreciated. I am very new to bioinformatics so apologies if it is due to a silly error on my part!! 

 

> txdb <- makeTxDbFromBiomart(biomart="ensembl", dataset="ecaballus_gene_ensembl",
+                             transcript_ids=NULL, circ_seqs=DEFAULT_CIRC_SEQS,
+                             filter=NULL, id_prefix="ensembl_",
+                             host="www.ensembl.org",
+                             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)  : 
  Failed to connect to ftp.ensembl.org port 21: Operation timed out

 

 


> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
[1] GenomicFeatures_1.30.3 AnnotationDbi_1.40.0   Biobase_2.38.0         GenomicRanges_1.30.3  
[5] GenomeInfoDb_1.14.0    IRanges_2.12.0         S4Vectors_0.16.0       BiocGenerics_0.24.0   
[9] biomaRt_2.34.2        

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.18               compiler_3.4.4             XVector_0.18.0             prettyunits_1.0.2         
 [5] bitops_1.0-6               tools_3.4.4                progress_1.2.0             zlibbioc_1.24.0           
 [9] digest_0.6.16              bit_1.1-14                 lattice_0.20-35            RSQLite_2.1.1             
[13] memoise_1.1.0              pkgconfig_2.0.2            rlang_0.2.2                Matrix_1.2-14             
[17] DelayedArray_0.4.1         DBI_1.0.0                  rstudioapi_0.7             curl_3.2                  
[21] GenomeInfoDbData_1.0.0     rtracklayer_1.38.3         stringr_1.3.1              httr_1.3.1                
[25] Biostrings_2.46.0          hms_0.4.2                  grid_3.4.4                 bit64_0.9-7               
[29] R6_2.2.2                   BiocParallel_1.12.0        XML_3.98-1.16              RMySQL_0.10.15            
[33] blob_1.1.1                 magrittr_1.5               matrixStats_0.54.0         GenomicAlignments_1.14.2  
[37] Rsamtools_1.30.0           SummarizedExperiment_1.8.1 assertthat_0.2.0           stringi_1.2.4             
[41] RCurl_1.95-4.11            crayon_1.3.4   

ADD COMMENTlink modified 10 days ago by James W. MacDonald47k • written 10 days ago by pat200
1
gravatar for James W. MacDonald
10 days ago by
United States
James W. MacDonald47k wrote:

You are using an unsupported version of R/Bioconductor. First try updating to the current version of R and Bioconductor and let us know if you still have the same error. You might also consider the AnnotationHub if you aren't tied to using EBI/Embl IDs:

> library(AnnotationHub)

> hub <- AnnotationHub()
snapshotDate(): 2018-04-30
> query(hub, c("equus caballus","orgdb"))
AnnotationHub with 2 records
# snapshotDate(): 2018-04-30
# $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Equus caballus, Equus caballus_przewalskii
# $rdataclass: OrgDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH62069"]]'

            title                                   
  AH62069 | org.Equus_caballus_przewalskii.eg.sqlite
  AH62112 | org.Equus_caballus.eg.sqlite
ADD COMMENTlink written 10 days ago by James W. MacDonald47k

Ugh. Missed the TxDb part of that.

> z <- query(hub, c("equus caballus","ensdb"))
> z
AnnotationHub with 6 records
# snapshotDate(): 2018-04-30
# $dataprovider: Ensembl
# $species: Equus Caballus
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH53202"]]'

            title                              
  AH53202 | Ensembl 87 EnsDb for Equus Caballus
  AH53706 | Ensembl 88 EnsDb for Equus Caballus
  AH56672 | Ensembl 89 EnsDb for Equus Caballus
  AH57747 | Ensembl 90 EnsDb for Equus Caballus
  AH60763 | Ensembl 91 EnsDb for Equus Caballus
  AH60967 | Ensembl 92 EnsDb for Equus Caballus
ADD REPLYlink written 10 days ago by James W. MacDonald47k

Thanks for this James. I should have check that before posting, my apologies! All working now. 

ADD REPLYlink modified 10 days ago • written 10 days ago by pat200
0
gravatar for Michael Love
10 days ago by
Michael Love19k
United States
Michael Love19k wrote:

 Can you re-post with the tag of the function’s package name: GenomicFeatures.

 This will alert the correct maintainers 

ADD COMMENTlink written 10 days ago by Michael Love19k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 137 users visited in the last hour