Hello!
I'm using qsea
to analyze my MBD-seq data.
I worked flawlessly until addPatternDensity
was performed.
It took almost a week to process my data consist of 2 bam files for KO and control.
Running on the multiple threads using BiocParallel
also took long time.
How can I speed up the process?
Thank you!!
> samples <- data.frame(sample_name = c("KO", "WT"),
file_name = c("KO.bam", "WT.bam"),
group = c("KO","WT"))
> path = wd
> samples$file_name=paste0(path,"/",samples$file_name )
> qseaSet = createQseaSet(sampleTable=samples,
BSgenome="BSgenome.Hsapiens.UCSC.hg38",
chr.select=paste0("chr", 1:22),
window_size=300)
> qseaSet = addCoverage(qseaSet, uniquePos=TRUE, paired=TRUE)
> qseaSet=addCNV(qseaSet, file_name="file_name",window_size=2e6,
paired=TRUE, parallel=FALSE, MeDIP=TRUE)
> qseaSet=addLibraryFactors(qseaSet)
> qseaSet=addPatternDensity(qseaSet, "CG", name="CpG")
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] qlcMatrix_0.9.7 sparsesvd_0.2 slam_0.1-48
[4] Matrix_1.2-18 reshape2_1.4.4 forcats_0.5.0
[7] dplyr_1.0.2 purrr_0.3.4 readr_1.4.0
[10] tidyr_1.1.2 tibble_3.0.4 tidyverse_1.3.0
[13] stringr_1.4.0 splitstackshape_1.4.8 patchwork_1.1.1
[16] pcaExplorer_2.16.0 ggpubr_0.4.0 ggrepel_0.9.0
[19] ggplot2_3.3.2 DESeq2_1.30.0 SummarizedExperiment_1.20.0
[22] Biobase_2.50.0 MatrixGenerics_1.2.0 matrixStats_0.57.0
[25] GenomicRanges_1.42.0 GenomeInfoDb_1.26.2 IRanges_2.24.1
[28] S4Vectors_0.28.1 BiocGenerics_0.36.0
loaded via a namespace (and not attached):
[1] GOstats_2.56.0 readxl_1.3.1 backports_1.2.1 BiocFileCache_1.14.0
[5] NMF_0.23.0 plyr_1.8.6 igraph_1.2.6 lazyeval_0.2.2
[9] GSEABase_1.52.1 shinydashboard_0.7.1 splines_4.0.3 BiocParallel_1.24.1
[13] crosstalk_1.1.0.1 gridBase_0.4-7 digest_0.6.27 foreach_1.5.1
[17] htmltools_0.5.0 viridis_0.5.1 GO.db_3.12.1 fansi_0.4.1
[21] magrittr_2.0.1 memoise_1.1.0 cluster_2.1.0 doParallel_1.0.16
[25] limma_3.46.0 openxlsx_4.2.3 annotate_1.68.0 modelr_0.1.8
[29] docopt_0.7.1 askpass_1.1 prettyunits_1.1.1 colorspace_2.0-0
[33] rvest_0.3.6 blob_1.2.1 rappdirs_0.3.1 haven_2.3.1
[37] xfun_0.19 crayon_1.3.4 RCurl_1.98-1.2 jsonlite_1.7.2
[41] graph_1.68.0 genefilter_1.72.0 survival_3.2-7 iterators_1.0.13
[45] glue_1.4.2 registry_0.5-1 gtable_0.3.0 zlibbioc_1.36.0
[49] XVector_0.30.0 webshot_0.5.2 DelayedArray_0.16.0 car_3.0-10
[53] Rgraphviz_2.34.0 abind_1.4-5 SparseM_1.78 scales_1.1.1
[57] pheatmap_1.0.12 DBI_1.1.0 rngtools_1.5 rstatix_0.6.0
[61] Rcpp_1.0.5 viridisLite_0.3.0 xtable_1.8-4 progress_1.2.2
[65] foreign_0.8-79 bit_4.0.4 DT_0.16 AnnotationForge_1.32.0
[69] htmlwidgets_1.5.3 httr_1.4.2 threejs_0.3.3 shinyAce_0.4.1
[73] RColorBrewer_1.1-2 ellipsis_0.3.1 pkgconfig_2.0.3 XML_3.99-0.5
[77] dbplyr_2.0.0 locfit_1.5-9.4 tidyselect_1.1.0 rlang_0.4.9
[81] later_1.1.0.1 AnnotationDbi_1.52.0 munsell_0.5.0 cellranger_1.1.0
[85] tools_4.0.3 cli_2.2.0 generics_0.1.0 RSQLite_2.2.1
[89] broom_0.7.3 shinyBS_0.61 evaluate_0.14 fastmap_1.0.1
[93] heatmaply_1.1.1 fs_1.5.0 knitr_1.30 bit64_4.0.5
[97] zip_2.1.1 dendextend_1.14.0 RBGL_1.66.0 mime_0.9
[101] xml2_1.3.2 biomaRt_2.46.0 compiler_4.0.3 rstudioapi_0.13
[105] plotly_4.9.2.2 curl_4.3 ggsignif_0.6.0 reprex_0.3.0
[109] geneplotter_1.68.0 stringi_1.5.3 lattice_0.20-41 vctrs_0.3.6
[113] pillar_1.4.7 lifecycle_0.2.0 data.table_1.13.4 bitops_1.0-6
[117] seriation_1.2-9 httpuv_1.5.4 R6_2.5.0 TSP_1.1-10
[121] promises_1.1.1 topGO_2.42.0 gridExtra_2.3 rio_0.5.16
[125] codetools_0.2-18 assertthat_0.2.1 Category_2.56.0 openssl_1.4.3
[129] pkgmaker_0.32.2 withr_2.3.0 GenomeInfoDbData_1.2.4 hms_0.5.3
[133] grid_4.0.3 rmarkdown_2.6 carData_3.0-4 lubridate_1.7.9.2
[137] shiny_1.5.0 base64enc_0.1-3