Hello I am using universalmotif and enrich_motifs. Things run smoothly on my PC but a larger dataset has forced me to move to a computer cluster with more available memory. I am having problems running shuffle_sequences on that HPC, it will crash even with a single, relatively short sequence.
Some very simple code (from the vignette) and the error message that appears instantly:
data(ArabidopsisPromoters) euler <- shuffle_sequences(ArabidopsisPromoters, k = 2, method = "euler") terminate called without an active exception Aborted (core dumped)
I am not getting any useful message that would guide me in troubleshooting this... I should specify I am running this on a single cpu with 50GB of RAM assigned. This runs absolutely fine on my PC installation (with R 4.1.1, Bioconductor 3.14, but universalmotif_1.12.2). I rolled back the version on the HPC to 1.12.2 (as on my PC) but it still quits abruptly. Any help would be greatly appreciated. Thanks. Alex
> sessionInfo() R version 4.1.0 (2021-05-18) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so locale:  LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C  LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8  LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8  LC_PAPER=en_CA.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats4 stats graphics grDevices utils datasets methods  base other attached packages:  universalmotif_1.12.3 BSgenome.Mmusculus.UCSC.mm9_1.4.0  BSgenome_1.62.0 rtracklayer_1.54.0  Biostrings_2.62.0 XVector_0.34.0  GenomicRanges_1.46.1 GenomeInfoDb_1.30.0  IRanges_2.28.0 S4Vectors_0.32.3  BiocGenerics_0.40.0 loaded via a namespace (and not attached):  SummarizedExperiment_1.24.0 tidyselect_1.1.1  purrr_0.3.4 lattice_0.20-45  colorspace_2.0-2 vctrs_0.3.8  generics_0.1.1 yaml_2.2.2  utf8_1.2.2 XML_3.99-0.8  rlang_1.0.0 pillar_1.6.5  glue_1.6.1 DBI_1.1.2  BiocParallel_1.28.3 matrixStats_0.61.0  GenomeInfoDbData_1.2.7 lifecycle_1.0.1  zlibbioc_1.40.0 MatrixGenerics_1.6.0  munsell_0.5.0 gtable_0.3.0  restfulr_0.0.13 Biobase_2.54.0  parallel_4.1.0 fansi_1.0.2  Rcpp_1.0.8 scales_1.1.1  DelayedArray_0.20.0 Rsamtools_2.10.0  rjson_0.2.21 ggplot2_3.3.5  dplyr_1.0.7 BiocIO_1.4.0  grid_4.1.0 cli_3.1.1  tools_4.1.0 bitops_1.0-7  magrittr_2.0.2 RCurl_1.98-1.5  tibble_3.1.6 crayon_1.4.2  pkgconfig_2.0.3 MASS_7.3-55  ellipsis_0.3.2 Matrix_1.4-0  assertthat_0.2.1 R6_2.5.1  GenomicAlignments_1.30.0 compiler_4.1.0