Question: Problem when constructing a TxDb with makeTxDbFromGFF:Error in dbGetQuery(conn,SQL) :
1
gravatar for Wet&DryImmunology
3.8 years ago by
Japan
Wet&DryImmunology220 wrote:

I was learning RNA-seq analysis following the RNA-seq workflow: gene-level exploratory analysis and differential expression. 

I came to the step of constructing a TxDb:

 

gtffile <- file.path(dir,"Homo_sapiens.GRCh37.75_subset.gtf")

> (txdb <- makeTxDbFromGFF(gtffile, format="gtf",circ_seqs=character()))

Import genomic features from the file as a GRanges object ... OK

Prepare the 'metadata' data frame ... OK

Make the TxDb object ... Warning messages:

1: 'BiocGenerics:::updateS4' is deprecated.

Use 'replaceSlots' instead.

See help("Deprecated") 

2: 'BiocGenerics:::updateS4' is deprecated.

Use 'replaceSlots' instead.

See help("Deprecated") 

3: 'BiocGenerics:::updateS4' is deprecated.

Use 'replaceSlots' instead.

See help("Deprecated") 

4: 'BiocGenerics:::updateS4' is deprecated.

Use 'replaceSlots' instead.

See help("Deprecated") 

Error in dbGetQuery(conn, SQL) : 

  error in evaluating the argument 'conn' in selecting a method for function 'dbGetQuery': Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : 

  object 'dbconn' not found

 

and:

> (ebg <- exonsBy(txdb,by="gene"))

Error in exonsBy(txdb, by = "gene") : 

  error in evaluating the argument 'x' in selecting a method for function 'exonsBy': Error: object 'txdb' not found

 

I guess that I could not ignore the error (and warning?)

Some people also had similar problem with makeTxDbFromGFF

https://support.bioconductor.org/p/70695/

he solved his problem through installing a new version of R and GenomicFeatures, but I don't think that could apply to my problem, for both my R and GenomicFeatures are new:

 

> sessionInfo()

R version 3.2.2 (2015-08-14)

Platform: x86_64-apple-darwin13.4.0 (64-bit)

Running under: OS X 10.9.5 (Mavericks)


locale:

[1] C/UTF-8/C/C/C/C


attached base packages:

[1] stats4    parallel  stats     graphics  grDevices utils     datasets 

[8] methods   base     


other attached packages:

 [1] GenomicFeatures_1.20.6 AnnotationDbi_1.30.1   Biobase_2.28.0        

 [4] Rsamtools_1.20.5       Biostrings_2.36.4      XVector_0.8.0         

 [7] airway_0.102.0         GenomicRanges_1.20.8   GenomeInfoDb_1.4.3    

[10] IRanges_2.4.0          S4Vectors_0.8.0        BiocGenerics_0.14.0   

[13] BiocInstaller_1.18.5  


loaded via a namespace (and not attached):

 [1] zlibbioc_1.14.0         GenomicAlignments_1.4.2 BiocParallel_1.2.22    

 [4] tools_3.2.2             DBI_0.3.1               lambda.r_1.1.7         

 [7] futile.logger_1.4.1     rtracklayer_1.28.10     futile.options_1.0.0   

[10] bitops_1.0-6            RCurl_1.95-4.7          biomaRt_2.24.1         

[13] RSQLite_1.0.0           XML_3.98-1.3           

Could anyone have any idea how to solve this problem?

Thanks very much!

 

Sorry I forgot to paste the traceback()

traceback()

13: dbGetQuery(conn, SQL)

12: AnnotationDbi:::dbEasyQuery(AnnotationDbi:::dbconn(annotationdb), 

        paste(sql, collapse = "\n"))

11: queryAnnotationDb(txdb, sql)

10: load_chrominfo(.self, set.col.class = TRUE)

9: .Object$initialize(...)

8: initialize(value, ...)

7: initialize(value, ...)

6: methods::new(def, ...)

5: .TxDb$new(conn = conn)

4: TxDb(conn)

3: makeTxDb(transcripts, splicings, genes = genes, chrominfo = chrominfo, 

       metadata = metadata, reassign.ids = TRUE)

2: makeTxDbFromGRanges(gr, metadata = metadata)

1: makeTxDbFromGFF(gtffile, format = "gtf", circ_seqs = character())

> (txdb <- makeTxDbFromGFF(gtffile, format="gtf",circ_seqs=character()))

Sorry that if some necessary information is left out, please kindly let me know if any further information is needed to evaluate the problem.

 

rna-seq R • 2.6k views
ADD COMMENTlink modified 17 months ago by Biostar ♦♦ 20 • written 3.8 years ago by Wet&DryImmunology220
2

It looks like GenomicFeatures has some problems, at least on Linux. You have a mix of bioconductor 3.1 (e.g., GenomicFeatures) and 3.2 (e.g., IRanges) packages, which is probably causing the problem.

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by Devon Ryan91k

Yes, actually,that is the problem. 

Thank you very much. Ryan. 

 

* Packages too new for Bioconductor version '3.1'

          Version
IRanges   "2.4.0"
S4Vectors "0.8.0"

 

ADD REPLYlink written 3.8 years ago by Wet&DryImmunology220
0
gravatar for Wet&DryImmunology
3.8 years ago by
Japan
Wet&DryImmunology220 wrote:

Problem solved. In case people have the same problem, please see the attached link. 

https://support.bioconductor.org/p/73482/

ADD COMMENTlink written 3.8 years ago by Wet&DryImmunology220
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