topicsRcisTarget lseek erro about cistopic

[cbravo93]

Hi!

Does it work lowering the number of cores (e.g. 5)?

[jk86754]

Same error, unfortunately.

[cbravo93]

And with feather 0.3.1?

[jk86754]

I am using feather 0.3.3

I can roll it back to 0.3.1 if that is what you recommend.

[jk86754]

Just an update: same error with feather 0.3.1

[cbravo93]

Can you try redownloading the database? You can find the instructions here: https://resources.aertslab.org/cistarget/help.html . And once you have it:

library(RcisTarget)
PathToFeather <- 'Your_path'
try <- importRankings(PathToFeather)

[jk86754]

Thanks. I re-downloaded the databases. However, now i get the error:

I do have feather installed and loaded (see sessionInfo()). So not sure what is going on here. I am working in a docker container using Rstudio; not sure if this causing the issue.

cisTopicObject <- topicsRcisTarget(cisTopicObject, genome='hg19', pathToFeather=pathToFeather, reduced_database=FALSE, nesThreshold=3, rocthr=0.005, maxRank=20000, nCores=5)
[1] "Exporting data to clusters..."
Error in checkForRemoteErrors(lapply(cl, recvResult)) :
5 nodes produced errors; first error: package or namespace load failed for ‘RcisTarget’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘feather’
In addition: Warning message:
In data(motifAnnotations_hgnc) : data set ‘motifAnnotations_hgnc’ not found
sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /sc/wo/app/R/v3.5.1/lib64/R/lib/libRblas.so
LAPACK: /sc/wo/app/R/v3.5.1/lib64/R/lib/libRlapack.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] parallel stats4 grid stats graphics grDevices utils
[8] datasets methods base

other attached packages:
[1] RcisTarget_1.5.0
[2] feather_0.3.3
[3] cisTopic_0.2.1
[4] BiocParallel_1.14.2
[5] doParallel_1.0.14
[6] iterators_1.0.10
[7] foreach_1.4.4
[8] densityClust_0.3
[9] org.Hs.eg.db_3.6.0
[10] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[11] GenomicFeatures_1.34.8
[12] AnnotationDbi_1.44.0
[13] Biobase_2.42.0
[14] ChIPseeker_1.18.0
[15] rGREAT_1.14.0
[16] GenomicRanges_1.34.0
[17] GenomeInfoDb_1.18.2
[18] IRanges_2.16.0
[19] S4Vectors_0.20.1
[20] BiocGenerics_0.28.0
[21] data.table_1.12.2
[22] fastcluster_1.1.25
[23] ComplexHeatmap_1.20.0
[24] Rtsne_0.15
[25] umap_0.2.2.0
[26] Rsubread_1.32.4

loaded via a namespace (and not attached):
[1] snow_0.4-3 circlize_0.4.6
[3] fastmatch_1.1-0 plyr_1.8.4
[5] igraph_1.2.2 lazyeval_0.2.2
[7] GSEABase_1.42.0 splines_3.5.1
[9] ggplot2_3.1.1 gridBase_0.4-7
[11] urltools_1.7.3 digest_0.6.18
[13] htmltools_0.3.6 GOSemSim_2.8.0
[15] viridis_0.5.1 GO.db_3.6.0
[17] gdata_2.18.0 lda_1.4.2
[19] magrittr_1.5 memoise_1.1.0
[21] Biostrings_2.48.0 annotate_1.60.1
[23] matrixStats_0.54.0 R.utils_2.8.0
[25] enrichplot_1.2.0 prettyunits_1.0.2
[27] colorspace_1.4-1 blob_1.1.1
[29] ggrepel_0.8.0 dplyr_0.7.8
[31] crayon_1.3.4 RCurl_1.95-4.12
[33] jsonlite_1.6 graph_1.60.0
[35] bindr_0.1.1 survival_2.44-1.1
[37] glue_1.3.1 polyclip_1.10-0
[39] gtable_0.3.0 zlibbioc_1.28.0
[41] XVector_0.22.0 UpSetR_1.4.0
[43] GetoptLong_0.1.7 DelayedArray_0.8.0
[45] shape_1.4.4 scales_1.0.0
[47] DOSE_3.8.2 DBI_1.0.0
[49] Rcpp_1.0.0 plotrix_3.7-5
[51] viridisLite_0.3.0 xtable_1.8-4
[53] progress_1.2.2 gridGraphics_0.4-1
[55] reticulate_1.10 bit_1.1-14
[57] europepmc_0.3 DT_0.6
[59] htmlwidgets_1.3 httr_1.4.0
[61] fgsea_1.8.0 FNN_1.1.2.1
[63] gplots_3.0.1.1 RColorBrewer_1.1-2
[65] R.methodsS3_1.7.1 pkgconfig_2.0.2
[67] XML_3.98-1.19 farver_1.1.0
[69] later_0.7.5 ggplotify_0.0.3
[71] tidyselect_0.2.5 rlang_0.3.4
[73] reshape2_1.4.3 munsell_0.5.0
[75] tools_3.5.1 RSQLite_2.1.1
[77] ggridges_0.5.1 stringr_1.4.0
[79] yaml_2.2.0 npsurv_0.4-0
[81] bit64_0.9-7 fitdistrplus_1.0-14
[83] caTools_1.17.1.1 purrr_0.3.2
[85] ggraph_1.0.2 bindrcpp_0.2.2
[87] mime_0.6 R.oo_1.22.0
[89] DO.db_2.9 xml2_1.2.0
[91] biomaRt_2.36.1 compiler_3.5.1
[93] rstudioapi_0.10 lsei_1.2-0
[95] tibble_2.1.1 tweenr_1.0.1
[97] stringi_1.2.4 lattice_0.20-38
[99] Matrix_1.2-17 pillar_1.4.0
[101] triebeard_0.3.0 GlobalOptions_0.1.0
[103] cowplot_0.9.4 bitops_1.0-6
[105] httpuv_1.4.5 AUCell_1.7.1
[107] rtracklayer_1.40.6 qvalue_2.14.1
[109] R6_2.4.0 promises_1.0.1
[111] KernSmooth_2.23-15 gridExtra_2.3
[113] codetools_0.2-16 boot_1.3-22
[115] MASS_7.3-51.4 gtools_3.8.1
[117] assertthat_0.2.1 SummarizedExperiment_1.10.1
[119] rjson_0.2.20 GenomicAlignments_1.18.1
[121] Rsamtools_1.32.3 GenomeInfoDbData_1.2.0
[123] doSNOW_1.0.16 hms_0.4.2
[125] rvcheck_0.1.3 ggforce_0.2.2
[127] shiny_1.2.0

[jk86754]

Just a quick update on this: I get the error above when having nCores set >1. A single core does not seem to throw this error. However, with a single core, this step is taking forever.

[cbravo93]

For the error above, can you try reinstalling RcisTarget?

Regards the initial error: It is indeed related to the reading of the databases; since they are huge (100Gb for human), I think it is resulting on memory issues when using more cores. We will look further on this!

[jk86754]

Thanks. For now, i just use a single core.