Question: genbankr fails when reading GBK file
gravatar for Monther Alhamdoosh
24 months ago by
Australia/Melbourne/CSL Limited
Monther Alhamdoosh40 wrote:

Hi Gabriel, 

I was trying to use your package to read a Genbank file but it failed with the following error: 

> gb = readGenBank(gbFile, verbose = TRUE)
Error in validObject(.Object) : 
  invalid class “GRanges” object: 'mcols(x)' is not parallel to 'x'
> traceback()
10: stop(msg, ": ", errors, domain = NA)
9: validObject(.Object)
8: initialize(value, ...)
7: initialize(value, ...)
6: new(Class, seqnames = seqnames, ranges = ranges, strand = strand, 
       elementMetadata = mcols, seqinfo = seqinfo)
5: new_GRanges("GRanges", seqnames = seqnames, ranges = ranges, 
       strand = strand, mcols = mcols, seqlengths = seqlengths, 
       seqinfo = seqinfo)
4: GRanges(seqnames = stk$seqnames, ranges = IRanges(start = stk$start, 
       end = stk$end), strand = stk$strand)
3: fill_stack_df(resthang$FEATURES[typs == "source"])
2: parseGenBank(text = text, partial = partial, verbose = verbose, 
       ret.seq = TRUE)
1: readGenBank(gbFile, verbose = TRUE)
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

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

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

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

other attached packages:
[1] genbankr_1.6.0       BiocInstaller_1.28.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.14               compiler_3.4.2             GenomeInfoDb_1.14.0       
 [4] XVector_0.18.0             GenomicFeatures_1.30.0     prettyunits_1.0.2         
 [7] bitops_1.0-6               tools_3.4.2                zlibbioc_1.24.0           
[10] progress_1.1.2             biomaRt_2.34.0             digest_0.6.12             
[13] bit_1.1-12                 BSgenome_1.46.0            lattice_0.20-35           
[16] RSQLite_2.0                memoise_1.1.0              tibble_1.3.4              
[19] rlang_0.1.4                Matrix_1.2-12              DelayedArray_0.4.1        
[22] DBI_0.7                    parallel_3.4.2             GenomeInfoDbData_0.99.1   
[25] rtracklayer_1.38.2         stringr_1.2.0              knitr_1.17                
[28] Biostrings_2.46.0          S4Vectors_0.16.0           IRanges_2.12.0            
[31] grid_3.4.2                 stats4_3.4.2               bit64_0.9-7               
[34] Biobase_2.38.0             R6_2.2.2                   AnnotationDbi_1.40.0      
[37] XML_3.98-1.9               RMySQL_0.10.13             BiocParallel_1.12.0       
[40] blob_1.1.0                 magrittr_1.5               matrixStats_0.52.2        
[43] GenomicAlignments_1.14.1   Rsamtools_1.30.0           BiocGenerics_0.24.0       
[46] GenomicRanges_1.30.0       SummarizedExperiment_1.8.0 assertthat_0.2.0          
[49] stringi_1.1.6              RCurl_1.95-4.8             VariantAnnotation_1.24.2  

Do you know what would be the reason for this error? 



genbankr • 354 views
ADD COMMENTlink modified 20 months ago by becker.gabriel10 • written 24 months ago by Monther Alhamdoosh40
Answer: genbankr fails when reading GBK file
gravatar for becker.gabriel
20 months ago by
becker.gabriel10 wrote:


Apologies for not responding sooner. I'm not familiar with this error. I haven't seen it before. Can you provide me the gbk file in question so I can do some debugging?



ADD COMMENTlink written 20 months ago by becker.gabriel10
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