RcisTarget error with multicore processing
1
1
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jka8119 ▴ 10
@jka8119-15080
Last seen 3.3 years ago

Hi,

 

I am getting the error below running 

> runSCENIC_2_createRegulons(scenicOptions)
05:53 Step 2. Identifying regulons
tfModulesSummary:

 top5perTarget top10perTarget           w005          top50 top50perTarget 
           198            531            870            944           1254 
          w001 
          1323 
05:53 RcisTarget: Calculating AUC
Scoring database:  [Source file: mm9-500bp-upstream-7species.mc9nr.feather]
Scoring database:  [Source file: mm9-tss-centered-10kb-7species.mc9nr.feather]
06:41 RcisTarget: Adding motif annotation
Error in .local(x, ...) : 
  cannot create 286 workers; 125 connections available in this session
Calls: runSCENIC_2_createRegulons ... bplapply -> bplapply -> bpstart -> bpstart -> .local
Execution halted
> sessionInfo()

R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.2 (Maipo)

Matrix products: default
BLAS: /sc/wo/app/R/v3.5.0/lib64/R/lib/libRblas.so
LAPACK: /sc/wo/app/R/v3.5.0/lib64/R/lib/libRlapack.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] SingleCellExperiment_1.2.0  SummarizedExperiment_1.10.1
 [3] DelayedArray_0.6.1          BiocParallel_1.14.1
 [5] matrixStats_0.53.1          Biobase_2.40.0
 [7] GenomicRanges_1.32.3        GenomeInfoDb_1.16.0
 [9] IRanges_2.14.10             S4Vectors_0.18.3
[11] BiocGenerics_0.26.0         RColorBrewer_1.1-2
[13] foreach_1.4.4               AUCell_1.2.4
[15] RcisTarget_1.0.2            SCENIC_0.99.0-03

loaded via a namespace (and not attached):
 [1] lattice_0.20-35        htmltools_0.3.6        blob_1.1.1
 [4] XML_3.98-1.11          rlang_0.2.1            R.oo_1.22.0
 [7] later_0.7.3            pillar_1.2.3           DBI_1.0.0
[10] R.utils_2.6.0          bit64_0.9-7            GenomeInfoDbData_1.1.0
[13] zlibbioc_1.26.0        R.methodsS3_1.7.1      codetools_0.2-15
[16] memoise_1.1.0          httpuv_1.4.4.1         AnnotationDbi_1.42.1
[19] GSEABase_1.42.0        Rcpp_0.12.17           xtable_1.8-2
[22] promises_1.0.1         feather_0.3.1          graph_1.58.0
[25] annotate_1.58.0        XVector_0.20.0         mime_0.5
[28] bit_1.1-14             hms_0.4.2              digest_0.6.15
[31] shiny_1.1.0            grid_3.5.0             tools_3.5.0
[34] bitops_1.0-6           magrittr_1.5           RCurl_1.95-4.10
[37] RSQLite_2.1.1          tibble_1.4.2           pkgconfig_2.0.1
[40] Matrix_1.2-14          data.table_1.11.4      iterators_1.0.9
[43] R6_2.2.2               compiler_3.5.0

Any help would be appreciated!

 

Joe

RcisTarget aucell SCENIC • 925 views
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@martin-morgan-1513
Last seen 9 days ago
United States

Try registering a default number of cores that you'd like to use, e.g.,

library(BiocParallel)
register(MulticoreParam(8))
runSCENIC_2_createRegulons(scenicOptions)

but actually I don't know where the script runSCENIC_2_createRegulons() comes from, so am only guessing...

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Thanks. The runSCENIC_2_createRegulons command is part of the latest version of SCENIC (https://github.com/aertslab/SCENIC)

Joe

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The help page suggests setting the number of cores as https://github.com/aertslab/SCENIC/blob/master/R/runSCENIC_2_createRegulons.R#L14

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Hello,

Thanks for the quick reply. Some other users also came up with similar errors, so I will update the tutorial to make it more explicit.

Thank you!

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Thanks for the help! I will try to run SCENIC with the multicore parameters adjusted as you suggested.

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