Question: Errors with makeTxDbFromBiomart
0
gravatar for gnani.science
2.2 years ago by
gnani.science0 wrote:

Hi

I'm trying to make a txDb object from biomart. 

When running this command:

The following error apperas....

txdb = makeTxDbFromBiomart (biomart="fungal_mart", dataset="mpoae_eg_gene", host="fungi.ensembl.org")

Download and preprocess the 'transcripts' data frame ... OK

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)  : 

  Server denied you to change to the given directory

In addition: Warning message:

call dbDisconnect() when finished working with a connection

 

Kindly help me...

 

Thanks in Advance..

with regards

Gnanendra

 

 

chip-seq • 496 views
ADD COMMENTlink modified 2.2 years ago by Hervé Pagès ♦♦ 14k • written 2.2 years ago by gnani.science0
Answer: Errors with makeTxDbFromBiomart
1
gravatar for Hervé Pagès
2.2 years ago by
Hervé Pagès ♦♦ 14k
United States
Hervé Pagès ♦♦ 14k wrote:

Hi Gnanendra,

Thanks for reporting this problem. Note that you should always tag your question with the package that is causing problem, which in this case is the GenomicFeatures package (where the makeTxDbFromBiomart() function belongs). The problem should now be fixed in GenomicFeatures 1.28.5.

Note that, as Mike pointed out, using makeTxDbFromGFF() works but please note that mpoae_eg_gene is the dataset for Magnaporthe poae, not for Magnaporthe oryzae. So the URL to the GFF3 file is:

gff3_url <- "ftp://ftp.ensemblgenomes.org/pub/fungi/current/gff3/magnaporthe_poae/Magnaporthe_poae.Mag_poae_ATCC_64411_V1.37.gff3.gz"

Anyway, I would recommend using makeTxDbFromBiomart() over makeTxDbFromGFF() here. You get the same set of transcripts but the former gives you the chromosome lengths and also better/cleaner transcript names:

library(GenomicFeatures)
txdb <- makeTxDbFromBiomart(biomart="fungal_mart",
                            dataset="mpoae_eg_gene",
                            host="fungi.ensembl.org")
txdb2 <- makeTxDbFromGFF(gff3_url)
length(transcripts(txdb))
# [1] 12760
length(transcripts(txdb2))
# [1] 12760
all(transcripts(txdb) == transcripts(txdb2))
# [1] TRUE

tail(transcripts(txdb))
# GRanges object with 6 ranges and 2 metadata columns:     
#            seqnames       ranges strand |     tx_id      tx_name
#               <Rle>    <IRanges>  <Rle> | <integer>  <character>
#   [1] supercont1.97 [2746, 3603]      - |     12755 MAPG_11970T0
#   [2] supercont1.98 [ 598, 5413]      + |     12756 MAPG_11974T0
#   [3] supercont1.98 [   1,  699]      - |     12757 MAPG_11973T0
#   [4] supercont1.98 [5439, 5647]      - |     12758 MAPG_11975T0
#   [5] supercont1.99 [1261, 5381]      + |     12759 MAPG_11977T0
#   [6] supercont1.99 [   1, 1191]      - |     12760 MAPG_11976T0
#   -------
#   seqinfo: 205 sequences from an unspecified genome

tail(transcripts(txdb2))
# GRanges object with 6 ranges and 2 metadata columns:                
#            seqnames       ranges strand |     tx_id                 tx_name
#               <Rle>    <IRanges>  <Rle> | <integer>             <character>
#   [1] supercont1.97 [2746, 3603]      - |     12755 transcript:MAPG_11970T0
#   [2] supercont1.98 [ 598, 5413]      + |     12756 transcript:MAPG_11974T0
#   [3] supercont1.98 [   1,  699]      - |     12757                    <NA>
#   [4] supercont1.98 [5439, 5647]      - |     12758 transcript:MAPG_11975T0
#   [5] supercont1.99 [1261, 5381]      + |     12759 transcript:MAPG_11977T0
#   [6] supercont1.99 [   1, 1191]      - |     12760                    <NA>
#   -------
#   seqinfo: 200 sequences from an unspecified genome; no seqlengths

GenomicFeatures 1.28.5 should become available via biocLite() in the next 48 hours.

Cheers,

H.

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Hervé Pagès ♦♦ 14k
Answer: Errors with makeTxDbFromBiomart
0
gravatar for Mike Smith
2.2 years ago by
Mike Smith4.0k
EMBL Heidelberg / de.NBI
Mike Smith4.0k wrote:

It doesn't look like makeTxDbFromBiomart() copes very well if you use a host that isn't www.ensembl.org.  It goes off and tries to find the metadata on an specific ftp site, and that fails when you're asking for a fungal genome.  Perhaps it's most straightforward to use makeTxDbFromGFF() instead.  You can give the address of the zipped version on the Ensembl Genomes ftp directly, e.g.

makeTxDbFromGFF(file = "ftp://ftp.ensemblgenomes.org/pub/fungi/release-37/gff3/magnaporthe_oryzae/Magnaporthe_oryzae.MG8.37.gff3.gz")
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: ftp://ftp.ensemblgenomes.org/pub/fungi/release-37/gff3/magnaporthe_oryzae/Magnaporthe_oryzae.MG8.37.gff3.gz
# Organism: NA
# Taxonomy ID: NA
# miRBase build ID: NA
# Genome: NA
# transcript_nrow: 13634
# exon_nrow: 36526
# cds_nrow: 34363
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2017-09-18 13:32:54 +0200 (Mon, 18 Sep 2017)
# GenomicFeatures version at creation time: 1.29.9
# RSQLite version at creation time: 2.0
# DBSCHEMAVERSION: 1.1
ADD COMMENTlink written 2.2 years ago by Mike Smith4.0k
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