Hi,
I am running bumphunter in an ubuntu server (443 G of RAM and 75 G of swap) on data from approx. 2000 EPIC arrays. This is the error I am getting when trying to run it with multicore: "Error in nulltabs[[i]] : subscript out of bounds". When running it with a single core, this error is not happening (but the process lasts two weeks, so this is not a solution).
This is my command line:
registerDoParallel( cores = 3)
res <- bumphunter(M.combat, design, coeff=2, chr= manifestInfo$chr, pos=manifestInfo$pos, maxGap=300, B=2000, cutoff=NULL, pickCutoff=TRUE, pickCutoffQ=0.995,nullMethod="bootstrap",verbose=TRUE)
[bumphunterEngine] Parallelizing using 3 workers/cores (backend: doParallelMC, version: 1.0.10).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Performing 2000 bootstraps.
[bumphunterEngine] Computing marginal bootstrap p-values.
[bumphunterEngine] cutoff: 0.085
[bumphunterEngine] Finding regions.
[bumphunterEngine] Found 11510 bumps.
[bumphunterEngine] Computing regions for each bootstrap.
[bumphunterEngine] Estimating p-values and FWER.
Error in nulltabs[[i]] : subscript out of bounds
This is my session info:
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=es_ES.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=es_ES.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 grid stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] bumphunter_1.20.0 locfit_1.5-9.1 iterators_1.0.9
[4] foreach_1.4.4 GenomicRanges_1.30.3 GenomeInfoDb_1.14.0
[7] IRanges_2.12.0 S4Vectors_0.16.0 BiocGenerics_0.24.0
[10] readstata13_0.9.0 readr_1.1.1 survey_3.33-2
[13] Matrix_1.2-12 foreign_0.8-70 Hmisc_4.1-1
[16] ggplot2_2.2.1 Formula_1.2-2 lattice_0.20-35
[19] survival_2.42-3
loaded via a namespace (and not attached):
[1] httr_1.3.1 Biobase_2.38.0
[3] RMySQL_0.10.14 bit64_0.9-7
[5] splines_3.4.4 assertthat_0.2.0
[7] latticeExtra_0.6-28 doRNG_1.6.6
[9] blob_1.1.1 Rsamtools_1.30.0
[11] GenomeInfoDbData_1.0.0 progress_1.1.2
[13] pillar_1.2.2 RSQLite_2.1.0
[15] backports_1.1.2 digest_0.6.15
[17] RColorBrewer_1.1-2 XVector_0.18.0
[19] checkmate_1.8.5 colorspace_1.3-2
[21] htmltools_0.3.6 plyr_1.8.4
[23] XML_3.98-1.11 pkgconfig_2.0.1
[25] biomaRt_2.34.2 zlibbioc_1.24.0
[27] xtable_1.8-2 scales_0.5.0
[29] BiocParallel_1.12.0 htmlTable_1.11.2
[31] tibble_1.4.2 pkgmaker_0.22
[33] SummarizedExperiment_1.8.1 GenomicFeatures_1.30.3
[35] nnet_7.3-12 lazyeval_0.2.1
[37] magrittr_1.5 memoise_1.1.0
[39] prettyunits_1.0.2 tools_3.4.4
[41] registry_0.5 data.table_1.10.4-3
[43] hms_0.4.2 matrixStats_0.53.1
[45] stringr_1.3.0 munsell_0.4.3
[47] cluster_2.0.6 rngtools_1.2.4
[49] DelayedArray_0.4.1 AnnotationDbi_1.40.0
[51] Biostrings_2.46.0 compiler_3.4.4
[53] rlang_0.2.0 RCurl_1.95-4.10
[55] rstudioapi_0.7 htmlwidgets_1.2
[57] bitops_1.0-6 base64enc_0.1-3
[59] gtable_0.2.0 codetools_0.2-15
[61] DBI_0.8 R6_2.2.2
[63] GenomicAlignments_1.14.2 gridExtra_2.3
[65] rtracklayer_1.38.3 knitr_1.20
[67] bit_1.1-12 stringi_1.1.7
[69] Rcpp_0.12.16 rpart_4.1-13
[71] acepack_1.4.1
Thanks!
Hi,
I also encountered the same problem. Have your problem been solved?
Thank you so much.
Best wishes,
Yu
HI, same problem for me. If you happen to get the solution, could you please post it.
Rgds, Alessandro