Comments (5)
Hi,
I'm on leave until April 26 and will not be dealing with GitHub issues during this time. @kasperdanielhansen may be able to help in the meantime.
Please provide a reproducible example and sessionInfo()
to help us help you.
Thanks,
Pete
from bsseq.
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] rhdf5_2.42.0 here_1.0.1
[3] plotly_4.10.1 PCAtools_2.10.0
[5] ggrepel_0.9.3 lubridate_1.9.2
[7] forcats_1.0.0 stringr_1.5.0
[9] dplyr_1.1.1 purrr_1.0.1
[11] readr_2.1.4 tidyr_1.3.0
[13] tibble_3.2.1 ggplot2_3.4.1
[15] tidyverse_2.0.0 MethylResolver_0.1.0
[17] methylSig_1.10.0 bsseq_1.34.0
[19] SummarizedExperiment_1.28.0 Biobase_2.58.0
[21] MatrixGenerics_1.10.0 matrixStats_0.63.0
[23] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
[25] IRanges_2.32.0 S4Vectors_0.36.2
[27] BiocGenerics_0.44.0
loaded via a namespace (and not attached):
[1] bitops_1.0-7 DSS_2.46.0
[3] httr_1.4.5 doParallel_1.0.17
[5] rprojroot_2.0.3 tools_4.2.1
[7] job_0.3.0 irlba_2.3.5.1
[9] utf8_1.2.3 R6_2.5.1
[11] HDF5Array_1.26.0 lazyeval_0.2.2
[13] colorspace_2.1-0 permute_0.9-7
[15] rhdf5filters_1.10.0 withr_2.5.0
[17] tidyselect_1.2.0 compiler_4.2.1
[19] cli_3.6.1 DelayedArray_0.24.0
[21] rtracklayer_1.58.0 scales_1.2.1
[23] DEoptimR_1.0-11 robustbase_0.95-1
[25] randomForest_4.7-1.1 digest_0.6.31
[27] Rsamtools_2.14.0 R.utils_2.12.2
[29] XVector_0.38.0 htmltools_0.5.5
[31] pkgconfig_2.0.3 sparseMatrixStats_1.10.0
[33] fastmap_1.1.1 limma_3.54.1
[35] BSgenome_1.66.3 htmlwidgets_1.6.2
[37] rlang_1.1.0 rstudioapi_0.14
[39] DelayedMatrixStats_1.20.0 BiocIO_1.8.0
[41] generics_0.1.3 jsonlite_1.8.4
[43] BiocParallel_1.32.5 gtools_3.9.4
[45] R.oo_1.25.0 BiocSingular_1.14.0
[47] RCurl_1.98-1.12 magrittr_2.0.3
[49] GenomeInfoDbData_1.2.9 Matrix_1.5-3
[51] Rcpp_1.0.10 munsell_0.5.0
[53] Rhdf5lib_1.20.0 fansi_1.0.4
[55] lifecycle_1.0.3 R.methodsS3_1.8.2
[57] stringi_1.7.12 Metrics_0.1.4
[59] yaml_2.3.7 zlibbioc_1.44.0
[61] plyr_1.8.8 grid_4.2.1
[63] dqrng_0.3.0 parallel_4.2.1
[65] crayon_1.5.2 doSNOW_1.0.20
[67] lattice_0.20-45 beachmat_2.14.0
[69] cowplot_1.1.1 Biostrings_2.66.0
[71] splines_4.2.1 hms_1.1.3
[73] locfit_1.5-9.7 pillar_1.9.0
[75] varhandle_2.0.5 rjson_0.2.21
[77] reshape2_1.4.4 ScaledMatrix_1.6.0
[79] codetools_0.2-19 XML_3.99-0.14
[81] glue_1.6.2 data.table_1.14.8
[83] vctrs_0.6.1 tzdb_0.3.0
[85] foreach_1.5.2 gtable_0.3.3
[87] rsvd_1.0.5 restfulr_0.0.15
[89] viridisLite_0.4.1 snow_0.4-4
[91] iterators_1.0.14 GenomicAlignments_1.34.0
[93] timechange_0.2.0
from bsseq.
And a reproducible example?
from bsseq.
Hmm I guess that'd be tough without sending you my cov files. I did end up getting it to work using SerialParam. Should I figure out a way to send my files if possible?
from bsseq.
If possible, that'd be helpful.
You'd only need to share the BSseq object (or a subset of it that is sufficient to reproduce the issue) rather than the .cov
files themselves.
How many cores does your machine have?
Can you try running it with BiocParallel::MulticoreParam(workers = k, progressbar = TRUE)
where you vary k
, e.g., k=1
, k=2
, k=4
, k=8
, k=16
to see if it works for smaller k
.
from bsseq.
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from bsseq.