Entering edit mode
Hi everyone,
I am running into this error with DiffBind that I have not had before.It is happening with multiple datasets. I have found similar threads with this issue but following those steps did not seem to solve it for me. I was wondering if anyone has any suggestions?
> Y1950_individual<-dba(sampleSheet = "Y1950_individual.csv",peakFormat='bed')
+ %>% dba.blacklist() %>% dba.count(bParallel=FALSE)
+ %>% dba.normalize() %>% dba.contrast()
+ %>% dba.analyze(bGreylist=FALSE)
Y1950_Proliferating_KSFMc Y1950 Cell-Type Proliferating KSFMc 1 raw
Y1950_Proliferating_KSFMc_Ca Y1950 Cell-Type Proliferating KSFMc_Ca 2 raw
Y1950_Proliferating_dKSFM Y1950 Cell-Type Proliferating dKSFM 3 raw
Y1950_Proliferating_dKSFM_Ca Y1950 Cell-Type Proliferating dKSFM_Ca 4 raw
Y1950_ContactInhibited_KSFMc Y1950 Cell-Type Contact_Inhibited KSFMc 1 raw
Y1950_ContactInhibited_KSFMc_Ca Y1950 Cell-Type Contact_Inhibited KSFMc_Ca 2 raw
Y1950_ContactInhibited_KSFMc_ABS_Ca Y1950 Cell-Type Contact_Inhibited KSFMc_ABS_Ca 3 raw
Y1950_ContactInhibited_dKSFM Y1950 Cell-Type Contact_Inhibited dKSFM 4 raw
Y1950_ContactInhibited_dKSFM_Ca Y1950 Cell-Type Contact_Inhibited dKSFM_Ca 5 raw
Y1950_ContactInhibited_dKSFM_Ca_TZ_BMS Y1950 Cell-Type Contact_Inhibited dKSFM_Ca_TZ_BMS 6 raw
Genome detected: Hsapiens.UCSC.hg38
Applying blacklist...
Removed: 951 of 1436436 intervals.
No control reads specified, unable to generate greylist.
Removed: 756 merged (of 1196097) and 98 (of 160034) consensus.
Computing summits...
Sample: reads/Y1950_Proliferating_R1.mLb.clN.sorted.bam125
Sample: reads/Y1950_Proliferating_R2.mLb.clN.sorted.bam125
Sample: reads/Y1950_Proliferating_R3.mLb.clN.sorted.bam125
Sample: reads/Y1950_Proliferating_R4.mLb.clN.sorted.bam125
Sample: reads/Y1950_ContactInhibited_R1.mLb.clN.sorted.bam125
Sample: reads/Y1950_ContactInhibited_R2.mLb.clN.sorted.bam125
Sample: reads/Y1950_ContactInhibited_R3.mLb.clN.sorted.bam125
Sample: reads/Y1950_ContactInhibited_R4.mLb.clN.sorted.bam125
Sample: reads/Y1950_ContactInhibited_R5.mLb.clN.sorted.bam125
Sample: reads/Y1950_ContactInhibited_R6.mLb.clN.sorted.bam125
Re-centering peaks...
Sample: reads/Y1950_Proliferating_R1.mLb.clN.sorted.bam125
Indexing reads/Y1950_Proliferating_R1.mLb.clN.sorted.bam
Reads will be counted as Paired-end.
'BiocParallel' did not register default BiocParallelParam:
missing value where TRUE/FALSE needed
'BiocParallel' did not register default BiocParallelParam:
missing value where TRUE/FALSE needed
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'assay': error in evaluating the argument 'BPPARAM' in selecting a method for function 'bplapply': attempt to select less than one element in get1index
sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.2.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] magrittr_2.0.2 DiffBind_3.4.9 SummarizedExperiment_1.24.0 Biobase_2.54.0
[5] MatrixGenerics_1.6.0 matrixStats_0.61.0 GenomicRanges_1.46.1 GenomeInfoDb_1.30.1
[9] IRanges_2.28.0 S4Vectors_0.32.3 BiocGenerics_0.40.0
loaded via a namespace (and not attached):
[1] bitops_1.0-7 bit64_4.0.5 httr_1.4.2 RColorBrewer_1.1-2
[5] numDeriv_2016.8-1.1 tools_4.1.2 utf8_1.2.2 R6_2.5.1
[9] irlba_2.3.5 KernSmooth_2.23-20 DBI_1.1.2 colorspace_2.0-2
[13] apeglm_1.16.0 DESeq2_1.34.0 tidyselect_1.1.1 bit_4.0.4
[17] compiler_4.1.2 cli_3.1.1 DelayedArray_0.20.0 rtracklayer_1.54.0
[21] caTools_1.18.2 scales_1.1.1 SQUAREM_2021.1 mvtnorm_1.1-3
[25] genefilter_1.76.0 mixsqp_0.3-43 stringr_1.4.0 digest_0.6.29
[29] Rsamtools_2.10.0 XVector_0.34.0 jpeg_0.1-9 pkgconfig_2.0.3
[33] htmltools_0.5.2 fastmap_1.1.0 invgamma_1.1 bbmle_1.0.24
[37] limma_3.50.0 BSgenome_1.62.0 htmlwidgets_1.5.4 rlang_1.0.1
[41] RSQLite_2.2.9 BiocIO_1.4.0 generics_0.1.2 hwriter_1.3.2
[45] BiocParallel_1.28.3 gtools_3.9.2 dplyr_1.0.8 RCurl_1.98-1.6
[49] GenomeInfoDbData_1.2.7 Matrix_1.4-0 Rcpp_1.0.8 munsell_0.5.0
[53] fansi_1.0.2 lifecycle_1.0.1 stringi_1.7.6 yaml_2.2.2
[57] MASS_7.3-55 zlibbioc_1.40.0 gplots_3.1.1 plyr_1.8.6
[61] blob_1.2.2 grid_4.1.2 parallel_4.1.2 ggrepel_0.9.1
[65] bdsmatrix_1.3-4 crayon_1.5.0 lattice_0.20-45 splines_4.1.2
[69] Biostrings_2.62.0 annotate_1.72.0 KEGGREST_1.34.0 locfit_1.5-9.4
[73] pillar_1.7.0 rjson_0.2.21 systemPipeR_2.0.5 geneplotter_1.72.0
[77] XML_3.99-0.8 glue_1.6.1 ShortRead_1.52.0 GreyListChIP_1.26.0
[81] latticeExtra_0.6-29 png_0.1-7 vctrs_0.3.8 gtable_0.3.0
[85] purrr_0.3.4 amap_0.8-18 assertthat_0.2.1 cachem_1.0.6
[89] ashr_2.2-47 ggplot2_3.3.5 emdbook_1.3.12 xtable_1.8-4
[93] restfulr_0.0.13 coda_0.19-4 survival_3.2-13 truncnorm_1.0-8
[97] tibble_3.1.6 memoise_2.0.1 AnnotationDbi_1.56.2 GenomicAlignments_1.30.0
[101] ellipsis_0.3.2
I have encountered exactly the same issue when I specified
bParallel=FALSEfor my ATAC-seq analysis. I have around 80000 peaks per sample (12 in total) and each BAM file is roughly 5 GB.I read similar threads on this forum and tried out solutions such as adding the following parameters to
dba.count():summits=FALSEandbUseSummarizeOverlaps=TRUEbut to no avail.When I do not specify
bParallel=FALSE, I get the following errors:Can any of these be caused by insufficient RAM? (My machine has 16 GB, DDR5).