BSGenome::getSeq gives error: Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append)
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@dborgesrmit-9232
Last seen 9.0 years ago
United States

Hello,

Whenever I try to use getSeq from the BSGenome package to fetch a sequence i get this error:

getSeq(BSgenome.Hsapiens.UCSC.hg19,"chr7")
Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
  subscript contains NAs or out-of-bounds indices

 

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] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.38.0                   Biostrings_2.38.1                 XVector_0.10.0                   
 [5] biomaRt_2.26.0                    rtracklayer_1.30.1                GenomicRanges_1.22.1              GenomeInfoDb_1.6.1               
 [9] IRanges_2.4.2                     S4Vectors_0.8.3                   BiocGenerics_0.16.1               reshape2_1.4.1                   
[13] ggplot2_1.0.1                     shiny_0.12.2                      BiocInstaller_1.20.1             

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.2                futile.logger_1.4.1        plyr_1.8.3                 futile.options_1.0.0       bitops_1.0-6               tools_3.2.2               
 [7] zlibbioc_1.16.0            digest_0.6.8               RSQLite_1.0.0              gtable_0.1.2               DBI_0.3.1                  proto_0.3-10              
[13] stringr_1.0.0              grid_3.2.2                 Biobase_2.30.0             R6_2.1.1                   AnnotationDbi_1.32.0       XML_3.98-1.3              
[19] BiocParallel_1.4.0         lambda.r_1.1.7             magrittr_1.5               GenomicAlignments_1.6.1    scales_0.3.0               Rsamtools_1.22.0          
[25] htmltools_0.2.6            MASS_7.3-45                SummarizedExperiment_1.0.1 mime_0.4                   xtable_1.8-0               colorspace_1.2-6          
[31] httpuv_1.3.3               stringi_1.0-1              RCurl_1.95-4.7             munsell_0.4.2 

 

bsgenome getseq • 2.4k views
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Actually, this happens also to other use cases of getSeq (the code below is taken from GenomicFeatures extractTranscriptSeqs help page):

library(GenomicFeatures)
library(BSgenome.Hsapiens.UCSC.hg19)
genome <- BSgenome.Hsapiens.UCSC.hg19

## Load a TxDb object:
txdb_file <- system.file("extdata", "hg19_knownGene_sample.sqlite",
                         package="GenomicFeatures")
txdb <- loadDb(txdb_file)

## Check that 'txdb' is based on the hg19 assembly:
txdb

## Extract the exon ranges grouped by transcript from 'txdb':
transcripts <- exonsBy(txdb, by="tx", use.names=TRUE)

## Extract the transcript sequences from the genome:
tx_seqs <- extractTranscriptSeqs(genome, transcripts)
tx_seqs

Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
  subscript contains NAs or out-of-bounds indices

 

Eventually this is caused by some updated package. I remember I did a package update today, but I can't remember which packages got updated (IRanges?).

Did you also update your packages recently?

cheers, jo

 

My session info:

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin15.0.0/x86_64 (64-bit)
Running under: OS X 10.11.2 (El Capitan)

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

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

other attached packages:
 [1] GenomicFeatures_1.22.4            AnnotationDbi_1.32.0             
 [3] Biobase_2.30.0                    BSgenome.Hsapiens.UCSC.hg19_1.4.0
 [5] BSgenome_1.38.0                   rtracklayer_1.30.1               
 [7] Biostrings_2.38.1                 XVector_0.10.0                   
 [9] GenomicRanges_1.22.1              GenomeInfoDb_1.6.1               
[11] IRanges_2.4.2                     S4Vectors_0.8.3                  
[13] BiocGenerics_0.16.1              

loaded via a namespace (and not attached):
 [1] zlibbioc_1.16.0            GenomicAlignments_1.6.1   
 [3] BiocParallel_1.4.0         tools_3.2.2               
 [5] SummarizedExperiment_1.0.1 DBI_0.3.1                 
 [7] lambda.r_1.1.7             futile.logger_1.4.1       
 [9] futile.options_1.0.0       bitops_1.0-6              
[11] biomaRt_2.26.0             RCurl_1.95-4.7            
[13] RSQLite_1.0.0              Rsamtools_1.22.0          
[15] XML_3.98-1.3        
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Entering edit mode
@martin-morgan-1513
Last seen 3 months ago
United States

I think it is A: IRanges/ShortRead causing crash?, a bad commit to IRanges 2.4.2 with a fix working it's way toward biocLite() or available now in svn.

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