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Question: Help with error produced when using makeTxDbFromBiomart
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gravatar for pat20
8 weeks 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 8 weeks ago by James W. MacDonald48k • written 8 weeks ago by pat200
1
gravatar for James W. MacDonald
8 weeks ago by
United States
James W. MacDonald48k 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 8 weeks ago by James W. MacDonald48k

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 8 weeks ago by James W. MacDonald48k

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

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by pat200
0
gravatar for Michael Love
8 weeks ago by
Michael Love20k
United States
Michael Love20k wrote:

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

 This will alert the correct maintainers 

ADD COMMENTlink written 8 weeks ago by Michael Love20k
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