Hello, I am trying to use the DiffBind package for ATACseq analysis. When I try to use the count() function to count peaks from bed files with reads R Studio crashes completely. Following previous posts I have tried the DBdata$config$RunParallel option and I now get the following error:
samples <- read.csv("samplesheettest3.csv") samples SampleID Tissue Factor Condition Treatment Replicate bamReads 1 B111 microglia NA WT 2 1 bedFilesfrombams/B111.bed.gz 2 B112 microglia NA WT 2 1 bedFilesfrombams/B112.bed.gz
DBdata <- dba(sampleSheet=samples) DBdata 2 Samples, 112676 sites in matrix (134672 total): ID Tissue Condition Treatment Replicate Caller Intervals 1 B111 microglia WT 2 1 narrow 128556 2 B112 microglia WT 2 1 narrow 120882
DBdata <- dba.count(DBdata, readFormat = DBAREADSBED, DBdata$config$RunParallel, FALSE) Error: Error processing one or more read files. Check warnings(). In addition: Warning messages: 1: In mclapply(arglist, fn, ..., mc.preschedule = TRUE, mc.allow.recursive = TRUE) : scheduled core 2 did not deliver a result, all values of the job will be affected 2:
I have checked my bed files and I think they are ok. I have tried with smalled bed files too (by selecting only lines from chr20 for example) but the same thing happens. Does anyone have any idea what could be the problem? and how to fix it?
sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.6
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale: [1] enGB.UTF-8/enGB.UTF-8/enGB.UTF-8/C/enGB.UTF-8/en_GB.UTF-8
attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] DiffBind2.14.0 SummarizedExperiment1.16.1 DelayedArray0.12.2 BiocParallel1.20.1
[5] matrixStats0.56.0 Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.1
[9] IRanges2.20.2 S4Vectors0.24.3 BiocGenerics_0.32.0
loaded via a namespace (and not attached):
[1] Category2.52.1 bitops1.0-6 bit640.9-7 RColorBrewer1.1-2 progress1.2.2
[6] httr1.4.1 Rgraphviz2.30.0 backports1.1.6 tools3.6.0 R62.4.1
[11] KernSmooth2.23-16 DBI1.1.0 colorspace1.4-1 withr2.1.2 tidyselect1.0.0
[16] prettyunits1.1.1 bit1.1-15.2 curl4.3 compiler3.6.0 graph1.64.0
[21] cli2.0.2 rtracklayer1.46.0 checkmate2.0.0 caTools1.18.0 scales1.1.0
[26] genefilter1.68.0 RBGL1.62.1 askpass1.1 rappdirs0.3.1 stringr1.4.0
[31] digest0.6.25 Rsamtools2.2.3 AnnotationForge1.28.0 XVector0.26.0 jpeg0.1-8.1
[36] pkgconfig2.0.3 BSgenome1.54.0 dbplyr1.4.2 limma3.42.2 rlang0.4.5
[41] rstudioapi0.11 RSQLite2.2.0 GOstats2.52.0 hwriter1.3.2 gtools3.8.2
[46] dplyr0.8.5 VariantAnnotation1.32.0 RCurl1.98-1.1 magrittr1.5 GO.db3.10.0
[51] GenomeInfoDbData1.2.2 Matrix1.2-18 Rcpp1.0.4.6 munsell0.5.0 fansi0.4.1
[56] lifecycle0.2.0 stringi1.4.6 yaml2.2.1 edgeR3.28.1 zlibbioc1.32.0
[61] gplots3.0.3 BiocFileCache1.10.2 grid3.6.0 blob1.2.1 ggrepel0.8.2
[66] gdata2.18.0 crayon1.3.4 lattice0.20-38 splines3.6.0 Biostrings2.54.0
[71] annotate1.64.0 GenomicFeatures1.38.2 hms0.5.3 batchtools0.9.13 locfit1.5-9.4
[76] pillar1.4.3 rjson0.2.20 systemPipeR1.20.0 base64url1.4 biomaRt2.42.1
[81] XML3.99-0.3 glue1.4.0 ShortRead1.44.3 latticeExtra0.6-29 data.table1.12.8
[86] vctrs0.2.4 png0.1-7 gtable0.3.0 openssl1.4.1 purrr0.3.3
[91] amap0.8-18 assertthat0.2.1 ggplot23.3.0 xtable1.8-4 survival3.1-11
[96] pheatmap1.0.12 tibble3.0.0 GenomicAlignments1.22.1 AnnotationDbi1.48.0 memoise1.1.0
[101] brew1.0-6 ellipsis0.3.0 GSEABase_1.48.0
