CHIPQC error regarding BiocParallel
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bioinfouser2 ▴ 10
@bioinfouser2-15147
Last seen 24 months ago

Hello,

I am trying to run ChIPQC on 83 samples. I am using the following line to make the DBA object:

CHIPQC_DBA = ChIPQC(samples,consensus = TRUE, bCount=TRUE, summits=250, annotation="hg38", blacklist = blacklist.hg38)

It is running until this point and crashing with the following error:

Checking chromosomes:
[1] "chr1"
Compiling annotation...
Adding controls...
Counting reads in consensus peakset...
Re-centering peaks...
Computing metrics for 83 samples...
'BiocParallel' did not register default BiocParallelParam:
  comparison of these types is not implemented
Error in if (!bpschedule(BPPARAM) || length(X) == 1L || bpnworkers(BPPARAM) ==  :
  missing value where TRUE/FALSE needed
Calls: ChIPQC -> bplapply -> bplapply -> bplapply -> bplapply
Execution halted

I would really appreciate if Rory or Thomas could help me on thise!

Here is my session info:

 R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

Matrix products: default
BLAS/LAPACK: /fshare/users/sakibs/miniconda3/envs/latest_R_3.6/lib/R/lib/libRblas.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] TxDb.Hsapiens.UCSC.hg38.knownGene_3.10.0
 [2] GenomicFeatures_1.38.2
 [3] AnnotationDbi_1.48.0
 [4] ChIPQC_1.22.0
 [5] DiffBind_2.14.0
 [6] SummarizedExperiment_1.16.1
 [7] DelayedArray_0.12.3
 [8] BiocParallel_1.20.1
 [9] matrixStats_0.56.0
[10] Biobase_2.46.0
[11] GenomicRanges_1.38.0
[12] GenomeInfoDb_1.22.1
[13] IRanges_2.20.2
[14] S4Vectors_0.24.4
[15] BiocGenerics_0.32.0
[16] ggplot2_3.3.0

loaded via a namespace (and not attached):
  [1] amap_0.8-18
  [2] colorspace_1.4-1
  [3] rjson_0.2.20
  [4] hwriter_1.3.2
  [5] ellipsis_0.3.0
  [6] XVector_0.26.0
  [7] ggrepel_0.8.2
  [8] bit64_0.9-7
  [9] fansi_0.4.1
 [10] splines_3.6.1
 [11] TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2
 [12] Nozzle.R1_1.1-1
 [13] Rsamtools_2.2.3
 [14] annotate_1.64.0
 [15] GO.db_3.10.0
 [16] dbplyr_1.4.3
 [17] png_0.1-7
 [18] pheatmap_1.0.12
 [19] graph_1.64.0
 [20] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2
 [21] compiler_3.6.1
 [22] httr_1.4.1
 [23] GOstats_2.52.0
 [24] backports_1.1.6
 [25] assertthat_0.2.1
 [26] Matrix_1.2-18
 [27] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [28] limma_3.42.2
 [29] cli_2.0.2
 [30] prettyunits_1.1.1
 [31] tools_3.6.1
 [32] gtable_0.3.0
 [33] glue_1.4.0
 [34] GenomeInfoDbData_1.2.2
 [35] Category_2.52.1
 [36] reshape2_1.4.4
 [37] systemPipeR_1.20.0
 [38] dplyr_0.8.5
 [39] batchtools_0.9.13
 [40] rappdirs_0.3.1
 [41] ShortRead_1.44.3
 [42] Rcpp_1.0.4.6
 [43] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
 [44] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2
 [45] vctrs_0.2.4
 [46] Biostrings_2.54.0
 [47] gdata_2.18.0
 [48] rtracklayer_1.46.0
 [49] TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0
 [50] stringr_1.4.0
 [51] lifecycle_0.2.0
 [52] gtools_3.8.2
 [53] XML_3.99-0.3
 [54] edgeR_3.28.1
 [55] zlibbioc_1.32.0
 [56] scales_1.1.0
 [57] BSgenome_1.54.0
 [58] VariantAnnotation_1.32.0
 [59] hms_0.5.3
 [60] RBGL_1.62.1
 [61] RColorBrewer_1.1-2
 [62] yaml_2.2.1
 [63] curl_4.3
 [64] memoise_1.1.0
 [65] biomaRt_2.42.1
 [66] latticeExtra_0.6-29
 [67] stringi_1.4.6
 [68] RSQLite_2.2.0
 [69] genefilter_1.68.0
 [70] checkmate_2.0.0
 [71] caTools_1.18.0
 [72] chipseq_1.36.0
 [73] rlang_0.4.5
 [74] pkgconfig_2.0.3
 [75] bitops_1.0-6
 [76] TxDb.Celegans.UCSC.ce6.ensGene_3.2.2
 [77] lattice_0.20-41
 [78] purrr_0.3.4
 [79] GenomicAlignments_1.22.1
 [80] bit_1.1-15.2
 [81] tidyselect_1.0.0
 [82] GSEABase_1.48.0
 [83] AnnotationForge_1.28.0
 [84] plyr_1.8.6
 [85] magrittr_1.5
 [86] R6_2.4.1
 [87] gplots_3.0.3
 [88] base64url_1.4
 [89] DBI_1.1.0
 [90] pillar_1.4.3
 [91] withr_2.1.2
 [92] survival_3.1-12
 [93] RCurl_1.98-1.2
 [94] tibble_3.0.0
 [95] crayon_1.3.4
 [96] KernSmooth_2.23-16
 [97] BiocFileCache_1.10.2
 [98] jpeg_0.1-8.1
 [99] progress_1.2.2
[100] locfit_1.5-9.4
[101] grid_3.6.1
[102] data.table_1.12.8
[103] blob_1.2.1
[104] Rgraphviz_2.30.0
[105] digest_0.6.25
[106] xtable_1.8-4
[107] brew_1.0-6
[108] openssl_1.4.1
[109] munsell_0.5.0
[110] askpass_1.1`
CHIPQC Diffbind chipseq rory stark Thomas Carroll • 717 views
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Also, this R environment I was using with conda in our linux cluster, with R version 3.6, where I could successfully install ChIPQC. But in our linux cluster, R 3.4.1 is installed and when I tried to install it there, it shows the following error:

` * caught segfault * address (nil), cause 'memory not mapped' An irrecoverable exception occurred. R is aborting now ... Segmentation fault (core dumped) ERROR: loading failed * removing ‘/fshare/users/sakibs/R/x86_64-pc-linux-gnu-library/3.4/ChIPQC’

* caught segfault * address (nil), cause 'memory not mapped'

Traceback: 1: q("no", status = status, runLast = FALSE) 2: doexit(status = status) 3: doexitonerror() 4: errmsg("loading failed") 5: doinstallsource(pkgname, instdir, pkg, desc) 6: doinstall(pkg) 7: tools:::.install_packages() An irrecoverable exception occurred. R is aborting now ... Segmentation fault (core dumped)`

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Rory Stark ★ 4.4k
@rory-stark-5741
Last seen 3 days ago
CRUK, Cambridge, UK

I have submitted a fix for ChIPQC that makes the use of BiocParallel more explicit, checking for installed backends and reporting information on how ChIPQC will be executed.

This fix will be in effect from version ChIPQC_1.32.1 in the main Release branch. There are related fixes in DiffBind_3.6.2 so these should be updated together.

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That's great! Can you please tell us where can we get the ChIPQC_1.32.1 version? Thanks!

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You need to be on the current version of Bioconductor, 3.15, which uses R version 4.2.0. Simply run:

BiocManager::install()

to update everything, which is perferred. Alternatively you can just update ChIPQC and DiffBind:

BiocManager::install(c("DiffBind", "ChIPQC"))
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Thanks so much for your reply. However, when I am running the code:

chipObj <- ChIPQC(samples, annotation="hg19")

I am getting the following error:

Error: BiocParallel errors 8 remote errors, element index: 1, 2, 3, 4, 5, 6, ... 0 unevaluated and other errors first remote error:

Error in if (is.na(blacklist)) blacklist = NULL: the condition has length > 1

However, when I run the following code it runs without any error:

chipObj <- ChIPQC(samples, annotation="hg19", blacklist = NULL)

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Entering edit mode

I've checked in another fix for this: ChIPQC_1.32.2.

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Thanks so much!

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