I'd like to first thank the developers for a fine set of tools. I am performing two-group comparison where each group contains 3~4 treated and input pairs. I am running the analysis on AWS EC2 in which I have installed r-base and DiffBind in a conda environment. I am currently trying to resolve the following issue from dba.analyze:
> h3k27ac <- dba.analyze(h3k27ac)
Applying Blacklist/Greylists...
Genome detected: Hsapiens.NCBI.GRCh38
Applying blacklist...
Removed: 5 of 58439 intervals.
Counting control reads for greylist...
Blacklist error: Error in value[[3L]](cond): GreyListChIP error: Error: BiocParallel errors
element index: 1, 2, 3, 4, 5, 6, ...
first error: 'seqlengths' contains NAs or negative values
Applying the blacklist works all right but greylist fails due to BiocParallel errors. From googling, I learned about the following but it did not help at all.
> BiocParallel::register(BiocParallel::SerialParam())
I know dba.analyze(h3k27ac, bGreylist=FALSE)
works but, given my input data, greylisting should have no issue from my perspective. I would appreciate any help or insight. Here's my sessionInfo FYI.
> sessionInfo( )
R version 4.1.0 (2021-05-18)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Amazon Linux 2
Matrix products: default
BLAS/LAPACK: /home/ec2-user/miniconda3/envs/R/lib/libopenblasp-r0.3.15.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 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] BiocParallel_1.26.1 DiffBind_3.2.4
[3] SummarizedExperiment_1.22.0 Biobase_2.52.0
[5] MatrixGenerics_1.4.0 matrixStats_0.59.0
[7] GenomicRanges_1.44.0 GenomeInfoDb_1.28.1
[9] IRanges_2.26.0 S4Vectors_0.30.0
[11] BiocGenerics_0.38.0
loaded via a namespace (and not attached):
[1] backports_1.2.1 GOstats_2.58.0 BiocFileCache_2.0.0
[4] plyr_1.8.6 GSEABase_1.54.0 splines_4.1.0
[7] ggplot2_3.3.5 amap_0.8-18 digest_0.6.27
[10] invgamma_1.1 GO.db_3.13.0 SQUAREM_2021.1
[13] fansi_0.5.0 magrittr_2.0.1 checkmate_2.0.0
[16] memoise_2.0.0 BSgenome_1.60.0 base64url_1.4
[19] limma_3.48.1 Biostrings_2.60.1 annotate_1.70.0
[22] systemPipeR_1.26.3 bdsmatrix_1.3-4 prettyunits_1.1.1
[25] jpeg_0.1-8.1 colorspace_2.0-2 blob_1.2.1
[28] rappdirs_0.3.3 apeglm_1.14.0 ggrepel_0.9.1
[31] dplyr_1.0.7 crayon_1.4.1 RCurl_1.98-1.3
[34] jsonlite_1.7.2 graph_1.70.0 genefilter_1.74.0
[37] brew_1.0-6 survival_3.2-11 VariantAnnotation_1.38.0
[40] glue_1.4.2 gtable_0.3.0 zlibbioc_1.38.0
[43] XVector_0.32.0 DelayedArray_0.18.0 V8_3.4.2
[46] Rgraphviz_2.36.0 scales_1.1.1 pheatmap_1.0.12
[49] mvtnorm_1.1-2 DBI_1.1.1 edgeR_3.34.0
[52] Rcpp_1.0.7 xtable_1.8-4 progress_1.2.2
[55] emdbook_1.3.12 bit_4.0.4 rsvg_2.1.2
[58] AnnotationForge_1.34.0 truncnorm_1.0-8 httr_1.4.2
[61] gplots_3.1.1 RColorBrewer_1.1-2 ellipsis_0.3.2
[64] pkgconfig_2.0.3 XML_3.99-0.6 dbplyr_2.1.1
[67] locfit_1.5-9.4 utf8_1.2.1 tidyselect_1.1.1
[70] rlang_0.4.11 AnnotationDbi_1.54.1 munsell_0.5.0
[73] tools_4.1.0 cachem_1.0.5 generics_0.1.0
[76] RSQLite_2.2.5 stringr_1.4.0 fastmap_1.1.0
[79] yaml_2.2.1 bit64_4.0.5 caTools_1.18.2
[82] purrr_0.3.4 KEGGREST_1.32.0 RBGL_1.68.0
[85] xml2_1.3.2 biomaRt_2.48.2 compiler_4.1.0
[88] rstudioapi_0.13 filelock_1.0.2 curl_4.3.2
[91] png_0.1-7 geneplotter_1.70.0 tibble_3.1.2
[94] stringi_1.7.3 GenomicFeatures_1.44.0 lattice_0.20-44
[97] Matrix_1.3-4 vctrs_0.3.8 pillar_1.6.1
[100] lifecycle_1.0.0 irlba_2.3.3 data.table_1.14.0
[103] bitops_1.0-7 rtracklayer_1.52.0 R6_2.5.0
[106] BiocIO_1.2.0 latticeExtra_0.6-29 hwriter_1.3.2
[109] ShortRead_1.50.0 KernSmooth_2.23-20 MASS_7.3-54
[112] gtools_3.9.2 assertthat_0.2.1 DESeq2_1.32.0
[115] Category_2.58.0 rjson_0.2.20 withr_2.4.2
[118] GenomicAlignments_1.28.0 batchtools_0.9.15 Rsamtools_2.8.0
[121] GenomeInfoDbData_1.2.6 hms_1.1.0 grid_4.1.0
[124] DOT_0.1 coda_0.19-4 GreyListChIP_1.24.0
[127] ashr_2.2-47 mixsqp_0.3-43 bbmle_1.0.23.1
[130] numDeriv_2016.8-1.1 restfulr_0.0.13
Hi Rory,
I am having this exact same problem and wonder if you had any other suggestions. I get the same error whether or not I run the blacklist before or after counting. I have my error below and also sessionInfo, but happy to provide more. My BAM files are from an alignment to GrCH37 and so I though this might be the issue - except that the blacklist functionality works fine with hg19..
Hello my friends, I have exactly the same issue. May I ask if you have already solve this problem? I have tried
library(BiocParallel) register(SerialParam())
but it did not work for me.Hi Rory let me know if you think this is a problem with control bam files. I can show you the bam files if you have time. Thank you so much!
Could you let me know the versions? Output of
sessionInfo()
.Hi Rory,
Thank you for your reply! Here is the my
sessionInfo()
:Please let me know what you think. I really appreciate your help!
R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.3 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 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
attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] BiocParallel_1.26.2 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.9
[5] purrr_0.3.4 readr_2.1.2 tidyr_1.2.0 tibble_3.1.7
[9] ggplot2_3.3.6 tidyverse_1.3.1 DiffBind_3.2.7 SummarizedExperiment_1.22.0 [13] Biobase_2.52.0 MatrixGenerics_1.4.3 matrixStats_0.62.0 GenomicRanges_1.44.0
[17] GenomeInfoDb_1.28.4 IRanges_2.26.0 S4Vectors_0.30.2 BiocGenerics_0.38.0
loaded via a namespace (and not attached): [1] readxl_1.4.0 backports_1.4.1 GOstats_2.58.0 BiocFileCache_2.0.0 plyr_1.8.7
[6] GSEABase_1.54.0 splines_4.1.2 amap_0.8-18 digest_0.6.29 invgamma_1.1
[11] GO.db_3.13.0 SQUAREM_2021.1 fansi_1.0.3 magrittr_2.0.3 checkmate_2.1.0
[16] memoise_2.0.1 BSgenome_1.60.0 base64url_1.4 tzdb_0.3.0 limma_3.48.3
[21] Biostrings_2.60.2 annotate_1.70.0 modelr_0.1.8 systemPipeR_1.26.3 bdsmatrix_1.3-4
[26] prettyunits_1.1.1 jpeg_0.1-9 colorspace_2.0-3 rvest_1.0.2 blob_1.2.3
[31] rappdirs_0.3.3 apeglm_1.14.0 ggrepel_0.9.1 haven_2.5.0 crayon_1.5.1
[36] RCurl_1.98-1.6 jsonlite_1.8.0 graph_1.70.0 genefilter_1.74.1 brew_1.0-7
[41] survival_3.3-1 VariantAnnotation_1.38.0 glue_1.6.2 gtable_0.3.0 zlibbioc_1.38.0
[46] XVector_0.32.0 DelayedArray_0.18.0 V8_4.2.0 Rgraphviz_2.36.0 scales_1.2.0
[51] pheatmap_1.0.12 mvtnorm_1.1-3 DBI_1.1.2 edgeR_3.34.1 Rcpp_1.0.8.3
[56] xtable_1.8-4 progress_1.2.2 emdbook_1.3.12 bit_4.0.4 rsvg_2.3.1
[61] AnnotationForge_1.34.1 truncnorm_1.0-8 httr_1.4.3 gplots_3.1.3 RColorBrewer_1.1-3
[66] ellipsis_0.3.2 pkgconfig_2.0.3 XML_3.99-0.9 dbplyr_2.1.1 locfit_1.5-9.5
[71] utf8_1.2.2 tidyselect_1.1.2 rlang_1.0.2 AnnotationDbi_1.54.1 cellranger_1.1.0
[76] munsell_0.5.0 tools_4.1.2 cachem_1.0.6 cli_3.3.0 generics_0.1.2
[81] RSQLite_2.2.14 broom_0.8.0 fastmap_1.1.0 yaml_2.3.5 fs_1.5.2
[86] bit64_4.0.5 caTools_1.18.2 KEGGREST_1.32.0 RBGL_1.68.0 xml2_1.3.3
[91] biomaRt_2.48.3 debugme_1.1.0 compiler_4.1.2 rstudioapi_0.13 filelock_1.0.2
[96] curl_4.3.2 png_0.1-7 reprex_2.0.1 stringi_1.7.6 GenomicFeatures_1.44.2
[101] lattice_0.20-45 Matrix_1.4-0 vctrs_0.4.1 pillar_1.7.0 lifecycle_1.0.1
[106] irlba_2.3.5 data.table_1.14.2 bitops_1.0-7 rtracklayer_1.52.1 R6_2.5.1
[111] BiocIO_1.2.0 latticeExtra_0.6-29 hwriter_1.3.2.1 ShortRead_1.50.0 KernSmooth_2.23-20
[116] MASS_7.3-55 gtools_3.9.2 assertthat_0.2.1 Category_2.58.0 rjson_0.2.21
[121] withr_2.5.0 GenomicAlignments_1.28.0 batchtools_0.9.15 Rsamtools_2.8.0 GenomeInfoDbData_1.2.6
[126] hms_1.1.1 grid_4.1.2 DOT_0.1 coda_0.19-4 GreyListChIP_1.24.0
[131] ashr_2.2-54 mixsqp_0.3-43 bbmle_1.0.25 lubridate_1.8.0 numDeriv_2016.8-1.1
[136] restfulr_0.0.13
The latest version,
DiffBind_3.6.1
, contains fixes for these issues. You will get these fixes if you upgrade toR_4.2.0
andBioconductor_3.15
.I am still getting an error in
DiffBind_3.6.1
:Seems like it might be a BPPARAM issue though...
Found the problem: link
You can overcome this issue by setting
mc.cores
: