Rsubread align --R session aborts
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sreekalasn • 0
@110f0c1f
Last seen 9 days ago
France

Hi,

I have been trying to align two different mouse reference genomes using Rsubread. The index was built successfully, but every time I ran align(), the R session aborts within seconds. I tried to run a single fastq file, thinking it could be the disk space, but I faced the same issue.

I have ran Rsubread in the past without any issues for the GRCm38.primary_assembly.genome, but now the R session crashes at the align() step. Any help will be highly appreciated. Thank you very much.

Index was built for the following reference genomes- 1) Mus_musculus_wsbeij.WSB_EiJ_v1.dna_sm.toplevel.fa.gz (primary assembly is not available yet) 2) GRCm38.primary_assembly.genome.fa.gz

The code to align WSB reference genome-

library(Rsubread)

buildindex(  
  basename = "WSBEiJ",
  reference = "Mus_musculus_wsbeij.WSB_EiJ_v1.dna_sm.toplevel.fa.gz",  
  gappedIndex = FALSE,
  indexSplit = FALSE,
  memory = 8000,
  TH_subread = 100,
  colorspace = FALSE)

#Read fastq files
 fastq.files.WSB_1 <-  list.files(path = "D:/PROJECTS/wsb_gz", full.names = TRUE)
 fastq.files.WSB_1[1:3]
  #[1] "D:/PROJECTS/wsb_gz/reads_10a-WSB-EiL-3d.fastq.gz"
  #[2] "D:/PROJECTS/wsb_gz/reads_10b-WSB-EiL-3d.fastq.gz"
  #[3] "D:/PROJECTS/wsb_gz/reads_11a-WSB-EiL-3d.fastq.gz"
  # 'a' and 'b' in the file name represent technical replicates. 

align(index="WSBEiJ", readfile1=fastq.files.WSB_1)

**###Here is where the R session aborts**


sessionInfo( )

R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3        rstudioapi_0.13     magrittr_2.0.3      munsell_0.5.0       tidyselect_1.1.2    colorspace_2.0-3   
 [7] R6_2.5.1            rlang_1.0.4         fansi_1.0.3         dplyr_1.0.9         tools_4.0.3         grid_4.0.3         
[13] gtable_0.3.0        xfun_0.30           tinytex_0.40        utf8_1.2.2          cli_3.3.0           DBI_1.1.3          
[19] assertthat_0.2.1    tibble_3.1.8        lifecycle_1.0.1     ggplot2_3.3.6       BiocManager_1.30.18 purrr_0.3.4        
[25] vctrs_0.4.1         ggrepel_0.9.1       glue_1.6.2          limma_3.46.0        compiler_4.0.3      pillar_1.8.0       
[31] scales_1.2.0        generics_0.1.3      pkgconfig_2.0.3
RNA Alignment Rsubread • 89 views
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Entering edit mode

Your R is very old. You will need to update to its latest version. Then you can install the latest Bioconductor and Rsubread and see if you still have this problem.

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