CHIPQC error regarding BiocParallel
1
0
Entering edit mode
bioinfouser2 ▴ 10
@bioinfouser2-15147
Last seen 4.2 years 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 • 2.3k views
ADD COMMENT
0
Entering edit mode

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)`

ADD REPLY
0
Entering edit mode
Rory Stark ★ 5.2k
@rory-stark-5741
Last seen 6 weeks ago
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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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"))
ADD REPLY
0
Entering edit mode

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)

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Thanks so much!

ADD REPLY

Login before adding your answer.

Traffic: 556 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6