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] # "D:/PROJECTS/wsb_gz/reads_10a-WSB-EiL-3d.fastq.gz" # "D:/PROJECTS/wsb_gz/reads_10b-WSB-EiL-3d.fastq.gz" # "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:  LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252  LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages:  stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached):  Rcpp_22.214.171.124 rstudioapi_0.13 magrittr_2.0.3 munsell_0.5.0 tidyselect_1.1.2 colorspace_2.0-3  R6_2.5.1 rlang_1.0.4 fansi_1.0.3 dplyr_1.0.9 tools_4.0.3 grid_4.0.3  gtable_0.3.0 xfun_0.30 tinytex_0.40 utf8_1.2.2 cli_3.3.0 DBI_1.1.3  assertthat_0.2.1 tibble_3.1.8 lifecycle_1.0.1 ggplot2_3.3.6 BiocManager_1.30.18 purrr_0.3.4  vctrs_0.4.1 ggrepel_0.9.1 glue_1.6.2 limma_3.46.0 compiler_4.0.3 pillar_1.8.0  scales_1.2.0 generics_0.1.3 pkgconfig_2.0.3