DiffBind dba.analyze never finishes

Question

[deemkd]

I'm running FAIREseq data through the most basic DiffBind pipeline in the tutorial and dba.analyze successfully goes through making final dispersion estimates, then never finishes. I don't think it's still running, it's been over an hour and R is using 0% of my CPU. Did I do something stupid and obvious or is some dependency not working properly, or something else? I'm not using any input control, which I've read is optional, is that causing an issue? Here's some details

contents of sample_sheet.csv

SampleID,Tissue,Factor,Condition,Treatment,Replicate,bamReads,Peaks,PeakCaller
DzSG_FAIRE_Rep1,DzSG,Dazao,none,FAIRE,1,../bam/Bmori_Dazao_SG_FAIRE_Rep1_std.bam,../macs2/Bmori_Dazao_SG_FAIRE_Rep1/Bmori_Dazao_SG_FAIRE_Rep1_peaks.narrowPeak,bed
DzSG_FAIRE_Rep2,DzSG,Dazao,none,FAIRE,2,../bam/Bmori_Dazao_SG_FAIRE_Rep2_std.bam,../macs2/Bmori_Dazao_SG_FAIRE_Rep2/Bmori_Dazao_SG_FAIRE_Rep2_peaks.narrowPeak,bed
DzSG_FAIRE_Rep3,DzSG,Dazao,none,FAIRE,3,../bam/Bmori_Dazao_SG_FAIRE_Rep3_std.bam,../macs2/Bmori_Dazao_SG_FAIRE_Rep3/Bmori_Dazao_SG_FAIRE_Rep3_peaks.narrowPeak,bed
D872SG_FAIRE_Rep1,D872SG,D872,none,FAIRE,1,../bam/Bmori_D872_SG_FAIRE_Rep1_std.bam,../macs2/Bmori_D872_SG_FAIRE_Rep1/Bmori_D872_SG_FAIRE_Rep1_peaks.narrowPeak,bed
D872SG_FAIRE_Rep2,D872SG,D872,none,FAIRE,2,../bam/Bmori_D872_SG_FAIRE_Rep2_std.bam,../macs2/Bmori_D872_SG_FAIRE_Rep2/Bmori_D872_SG_FAIRE_Rep2_peaks.narrowPeak,bed
D872SG_FAIRE_Rep3,D872SG,D872,none,FAIRE,3,../bam/Bmori_D872_SG_FAIRE_Rep3_std.bam,../macs2/Bmori_D872_SG_FAIRE_Rep3/Bmori_D872_SG_FAIRE_Rep3_peaks.narrowPeak,bed
DzBmE_FAIRE_Rep1,DzBmE,Dazao,none,FAIRE,1,../bam/Bmori_Dazao_BmE_FAIRE_Rep1_std.bam,../macs2/Bmori_Dazao_BmE_FAIRE_Rep1/Bmori_Dazao_BmE_FAIRE_Rep1_peaks.narrowPeak,bed
DzBmE_FAIRE_Rep2,DzBmE,Dazao,none,FAIRE,2,../bam/Bmori_Dazao_BmE_FAIRE_Rep2_std.bam,../macs2/Bmori_Dazao_BmE_FAIRE_Rep2/Bmori_Dazao_BmE_FAIRE_Rep2_peaks.narrowPeak,bed
DzBmE_FAIRE_Rep3,DzBmE,Dazao,none,FAIRE,3,../bam/Bmori_Dazao_BmE_FAIRE_Rep3_std.bam,../macs2/Bmori_Dazao_BmE_FAIRE_Rep3/Bmori_Dazao_BmE_FAIRE_Rep3_peaks.narrowPeak,bed

commands in R:

library(DiffBind)

library(rtracklayer)

bm_faire <- dba(sampleSheet="sample_sheet.csv")

bm_faire <- dba.count(bm_faire)

bm_faire <- dba.normalize(bm_faire)

bm_faire <- dba.contrast(bm_faire, categories=DBA_TISSUE)

bm_faire <- dba.analyze(bm_faire)

output from final line:

Applying Blacklist/Greylists...

No genome detected.

Analyzing...
gene-wise dispersion estimates

mean-dispersion relationship

final dispersion estimates

Has anyone else experienced this? Any ideas?

[Rory Stark]

What platform are you running (Windows, Mac, Linux)? It would help to see the output of sessionInfo() to know all the software versions you are using.

If you get send me a link where I could get access to your DBA object bm_faire after the call to dba.contrast but before calling dba.analyze(), I could see if I can reproduce this.

[deemkd]

Dr. Stark, Thank you for your reply, I am not sure where/how to host/upload/link you my DBA object, but I would be glad to if you could direct me. The session info is:

R version 4.0.3 (2020-10-10) Platform: x86_64-apple-darwin20.2.0 (64-bit) Running under: macOS 11.1

Matrix products: default BLAS: /usr/local/Cellar/openblas/0.3.13/lib/libopenblasp-r0.3.13.dylib LAPACK: /usr/local/Cellar/r/4.0.3_2/lib/R/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] DiffBind_3.0.10 SummarizedExperiment_1.20.0 [3] Biobase_2.50.0 MatrixGenerics_1.2.0
[5] matrixStats_0.57.0 GenomicRanges_1.42.0
[7] GenomeInfoDb_1.26.2 IRanges_2.24.1
[9] S4Vectors_0.28.1 BiocGenerics_0.36.0

loaded via a namespace (and not attached): [1] amap_0.8-18 colorspace_2.0-0 rjson_0.2.20
[4] hwriter_1.3.2 ellipsis_0.3.1 XVector_0.30.0
[7] ggrepel_0.9.0 bit64_4.0.5 mvtnorm_1.1-1
[10] apeglm_1.12.0 AnnotationDbi_1.52.0 xml2_1.3.2
[13] splines_4.0.3 jsonlite_1.7.2 Rsamtools_2.6.0
[16] annotate_1.68.0 ashr_2.2-47 GO.db_3.12.1
[19] dbplyr_2.0.0 png_0.1-7 GreyListChIP_1.22.0
[22] pheatmap_1.0.12 graph_1.68.0 compiler_4.0.3
[25] httr_1.4.2 GOstats_2.56.0 backports_1.2.1
[28] assertthat_0.2.1 Matrix_1.3-2 limma_3.46.0
[31] prettyunits_1.1.1 tools_4.0.3 coda_0.19-4
[34] gtable_0.3.0 glue_1.4.2 GenomeInfoDbData_1.2.4
[37] Category_2.56.0 systemPipeR_1.24.2 dplyr_1.0.2
[40] rsvg_2.1 batchtools_0.9.15 rappdirs_0.3.1
[43] V8_3.4.0 ShortRead_1.48.0 Rcpp_1.0.5
[46] bbmle_1.0.23.1 vctrs_0.3.6 Biostrings_2.58.0
[49] rtracklayer_1.50.0 stringr_1.4.0 irlba_2.3.3
[52] lifecycle_0.2.0 gtools_3.8.2 XML_3.99-0.5
[55] edgeR_3.32.0 MASS_7.3-53 zlibbioc_1.36.0
[58] scales_1.1.1 BSgenome_1.58.0 VariantAnnotation_1.36.0 [61] hms_1.0.0 RBGL_1.66.0 RColorBrewer_1.1-2
[64] yaml_2.2.1 curl_4.3 memoise_1.1.0
[67] ggplot2_3.3.3 emdbook_1.3.12 bdsmatrix_1.3-4
[70] biomaRt_2.46.0 SQUAREM_2021.1 latticeExtra_0.6-29
[73] stringi_1.5.3 RSQLite_2.2.2 genefilter_1.72.0
[76] checkmate_2.0.0 GenomicFeatures_1.42.1 caTools_1.18.1
[79] BiocParallel_1.24.1 DOT_0.1 truncnorm_1.0-8
[82] rlang_0.4.10 pkgconfig_2.0.3 bitops_1.0-6
[85] invgamma_1.1 lattice_0.20-41 purrr_0.3.4
[88] GenomicAlignments_1.26.0 bit_4.0.4 tidyselect_1.1.0
[91] GSEABase_1.52.1 AnnotationForge_1.32.0 plyr_1.8.6
[94] magrittr_2.0.1 R6_2.5.0 gplots_3.1.1
[97] generics_0.1.0 base64url_1.4 DelayedArray_0.16.0
[100] DBI_1.1.0 pillar_1.4.7 withr_2.3.0
[103] mixsqp_0.3-43 survival_3.2-7 RCurl_1.98-1.2
[106] tibble_3.0.4 crayon_1.3.4 KernSmooth_2.23-18
[109] BiocFileCache_1.14.0 jpeg_0.1-8.1 progress_1.2.2
[112] locfit_1.5-9.4 grid_4.0.3 data.table_1.13.6
[115] blob_1.2.1 Rgraphviz_2.34.0 digest_0.6.27
[118] xtable_1.8-4 numDeriv_2016.8-1.1 brew_1.0-6
[121] openssl_1.4.3 munsell_0.5.0 askpass_1.1

[Zhuqiang]

Same problem. Any suggestions? Thanks!

sessionInfo() R version 4.3.1 (2023-06-16) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: AlmaLinux 8.8 (Sapphire Caracal)

Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblaso-r0.3.15.so; LAPACK version 3.9.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Asia/Shanghai tzcode source: system (glibc)

attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] DiffBind_3.10.1 SummarizedExperiment_1.30.2 Biobase_2.60.0 MatrixGenerics_1.12.3 matrixStats_1.0.0
[6] GenomicRanges_1.52.0 GenomeInfoDb_1.36.2 IRanges_2.34.1 S4Vectors_0.38.2 BiocGenerics_0.46.0

loaded via a namespace (and not attached): [1] amap_0.8-19 tidyselect_1.2.0 dplyr_1.1.3 Biostrings_2.68.1 bitops_1.0-7
[6] fastmap_1.1.1 RCurl_1.98-1.12 apeglm_1.22.1 GenomicAlignments_1.36.0 XML_3.99-0.14
[11] digest_0.6.33 lifecycle_1.0.3 invgamma_1.1 magrittr_2.0.3 compiler_4.3.1
[16] rlang_1.1.1 tools_4.3.1 utf8_1.2.3 yaml_2.3.7 rtracklayer_1.60.1
[21] S4Arrays_1.0.6 htmlwidgets_1.6.2 interp_1.1-4 DelayedArray_0.26.7 plyr_1.8.8
[26] RColorBrewer_1.1-3 ShortRead_1.58.0 abind_1.4-5 BiocParallel_1.34.2 KernSmooth_2.23-22
[31] numDeriv_2016.8-1.1 hwriter_1.3.2.1 grid_4.3.1 fansi_1.0.5 latticeExtra_0.6-30
[36] caTools_1.18.2 colorspace_2.1-0 ggplot2_3.4.3 scales_1.2.1 gtools_3.9.4
[41] MASS_7.3-60 bbmle_1.0.25 cli_3.6.1 mvtnorm_1.2-3 crayon_1.5.2
[46] generics_0.1.3 rstudioapi_0.15.0 rjson_0.2.21 bdsmatrix_1.3-6 stringr_1.5.0
[51] zlibbioc_1.46.0 parallel_4.3.1 restfulr_0.0.15 XVector_0.40.0 vctrs_0.6.3
[56] Matrix_1.6-1.1 mixsqp_0.3-48 ggrepel_0.9.3 irlba_2.3.5.1 systemPipeR_2.6.3
[61] jpeg_0.1-10 locfit_1.5-9.8 limma_3.56.2 glue_1.6.2 emdbook_1.3.13
[66] codetools_0.2-19 stringi_1.7.12 gtable_0.3.4 deldir_1.0-9 BiocIO_1.10.0
[71] munsell_0.5.0 tibble_3.2.1 pillar_1.9.0 htmltools_0.5.6 gplots_3.1.3
[76] BSgenome_1.68.0 GenomeInfoDbData_1.2.10 truncnorm_1.0-9 R6_2.5.1 GreyListChIP_1.32.1
[81] lattice_0.21-8 png_0.1-8 Rsamtools_2.16.0 SQUAREM_2021.1 ashr_2.2-63
[86] Rcpp_1.0.11 coda_0.19-4 DESeq2_1.40.2 pkgconfig_2.0.3

[Rory Stark]

Does the same thing happen if you run dba.analyze() with bParallel=FALSE? How about with method=DBA_EDGER?

Answer 1

[Rory Stark]

Did you ever get this resolved? If you send me a link so I can look at your DBA object, I cac see if I can reproduce the error.

I'd need the blacklists to have been run, so you could run the following code:

bm_faire <- dba(sampleSheet="sample_sheet.csv")
bm_faire <- dba.count(bm_faire)
bm_faire <- dba.normalize(bm_faire)
bm_faire <- dba.contrast(bm_faire, categories=DBA_TISSUE)
bm_faire <- dba.blacklist(db_faire)

Confirm that bm_faire <- dba.analyze(bm_faire) still fails to return, then send me a link to bm_faire.

Answer 2

[441559287]

This problem also occurs when I use diffbind under windows, but when I use diffbind under Linux, it will calculate quickly