BiocParallel error when running DiffBind
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1
Entering edit mode
r.finn ▴ 10
@rfinn-23243
Last seen 7 weeks ago
United Kingdom

Hi everyone,

I am running into this error with DiffBind that I have not had before.It is happening with multiple datasets. I have found similar threads with this issue but following those steps did not seem to solve it for me. I was wondering if anyone has any suggestions?

> Y1950_individual<-dba(sampleSheet = "Y1950_individual.csv",peakFormat='bed') 
+ %>% dba.blacklist() %>% dba.count(bParallel=FALSE) 
+ %>% dba.normalize() %>% dba.contrast() 
+ %>% dba.analyze(bGreylist=FALSE)

Y1950_Proliferating_KSFMc Y1950 Cell-Type Proliferating KSFMc 1 raw
Y1950_Proliferating_KSFMc_Ca Y1950 Cell-Type Proliferating KSFMc_Ca 2 raw
Y1950_Proliferating_dKSFM Y1950 Cell-Type Proliferating dKSFM 3 raw
Y1950_Proliferating_dKSFM_Ca Y1950 Cell-Type Proliferating dKSFM_Ca 4 raw
Y1950_ContactInhibited_KSFMc Y1950 Cell-Type Contact_Inhibited KSFMc 1 raw
Y1950_ContactInhibited_KSFMc_Ca Y1950 Cell-Type Contact_Inhibited KSFMc_Ca 2 raw
Y1950_ContactInhibited_KSFMc_ABS_Ca Y1950 Cell-Type Contact_Inhibited KSFMc_ABS_Ca 3 raw
Y1950_ContactInhibited_dKSFM Y1950 Cell-Type Contact_Inhibited dKSFM 4 raw
Y1950_ContactInhibited_dKSFM_Ca Y1950 Cell-Type Contact_Inhibited dKSFM_Ca 5 raw
Y1950_ContactInhibited_dKSFM_Ca_TZ_BMS Y1950 Cell-Type Contact_Inhibited dKSFM_Ca_TZ_BMS 6 raw
Genome detected: Hsapiens.UCSC.hg38
Applying blacklist...
Removed: 951 of 1436436 intervals.
No control reads specified, unable to generate greylist.
Removed: 756 merged (of 1196097) and 98 (of 160034) consensus.
Computing summits...
Sample: reads/Y1950_Proliferating_R1.mLb.clN.sorted.bam125 
Sample: reads/Y1950_Proliferating_R2.mLb.clN.sorted.bam125 
Sample: reads/Y1950_Proliferating_R3.mLb.clN.sorted.bam125 
Sample: reads/Y1950_Proliferating_R4.mLb.clN.sorted.bam125 
Sample: reads/Y1950_ContactInhibited_R1.mLb.clN.sorted.bam125 
Sample: reads/Y1950_ContactInhibited_R2.mLb.clN.sorted.bam125 
Sample: reads/Y1950_ContactInhibited_R3.mLb.clN.sorted.bam125 
Sample: reads/Y1950_ContactInhibited_R4.mLb.clN.sorted.bam125 
Sample: reads/Y1950_ContactInhibited_R5.mLb.clN.sorted.bam125 
Sample: reads/Y1950_ContactInhibited_R6.mLb.clN.sorted.bam125 
Re-centering peaks...
Sample: reads/Y1950_Proliferating_R1.mLb.clN.sorted.bam125 
Indexing reads/Y1950_Proliferating_R1.mLb.clN.sorted.bam
Reads will be counted as Paired-end.
'BiocParallel' did not register default BiocParallelParam:
  missing value where TRUE/FALSE needed
'BiocParallel' did not register default BiocParallelParam:
  missing value where TRUE/FALSE needed
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'assay': error in evaluating the argument 'BPPARAM' in selecting a method for function 'bplapply': attempt to select less than one element in get1index


sessionInfo()

R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.2.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

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

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

other attached packages:
 [1] magrittr_2.0.2              DiffBind_3.4.9              SummarizedExperiment_1.24.0 Biobase_2.54.0             
 [5] MatrixGenerics_1.6.0        matrixStats_0.61.0          GenomicRanges_1.46.1        GenomeInfoDb_1.30.1        
 [9] IRanges_2.28.0              S4Vectors_0.32.3            BiocGenerics_0.40.0        

loaded via a namespace (and not attached):
  [1] bitops_1.0-7             bit64_4.0.5              httr_1.4.2               RColorBrewer_1.1-2      
  [5] numDeriv_2016.8-1.1      tools_4.1.2              utf8_1.2.2               R6_2.5.1                
  [9] irlba_2.3.5              KernSmooth_2.23-20       DBI_1.1.2                colorspace_2.0-2        
 [13] apeglm_1.16.0            DESeq2_1.34.0            tidyselect_1.1.1         bit_4.0.4               
 [17] compiler_4.1.2           cli_3.1.1                DelayedArray_0.20.0      rtracklayer_1.54.0      
 [21] caTools_1.18.2           scales_1.1.1             SQUAREM_2021.1           mvtnorm_1.1-3           
 [25] genefilter_1.76.0        mixsqp_0.3-43            stringr_1.4.0            digest_0.6.29           
 [29] Rsamtools_2.10.0         XVector_0.34.0           jpeg_0.1-9               pkgconfig_2.0.3         
 [33] htmltools_0.5.2          fastmap_1.1.0            invgamma_1.1             bbmle_1.0.24            
 [37] limma_3.50.0             BSgenome_1.62.0          htmlwidgets_1.5.4        rlang_1.0.1             
 [41] RSQLite_2.2.9            BiocIO_1.4.0             generics_0.1.2           hwriter_1.3.2           
 [45] BiocParallel_1.28.3      gtools_3.9.2             dplyr_1.0.8              RCurl_1.98-1.6          
 [49] GenomeInfoDbData_1.2.7   Matrix_1.4-0             Rcpp_1.0.8               munsell_0.5.0           
 [53] fansi_1.0.2              lifecycle_1.0.1          stringi_1.7.6            yaml_2.2.2              
 [57] MASS_7.3-55              zlibbioc_1.40.0          gplots_3.1.1             plyr_1.8.6              
 [61] blob_1.2.2               grid_4.1.2               parallel_4.1.2           ggrepel_0.9.1           
 [65] bdsmatrix_1.3-4          crayon_1.5.0             lattice_0.20-45          splines_4.1.2           
 [69] Biostrings_2.62.0        annotate_1.72.0          KEGGREST_1.34.0          locfit_1.5-9.4          
 [73] pillar_1.7.0             rjson_0.2.21             systemPipeR_2.0.5        geneplotter_1.72.0      
 [77] XML_3.99-0.8             glue_1.6.1               ShortRead_1.52.0         GreyListChIP_1.26.0     
 [81] latticeExtra_0.6-29      png_0.1-7                vctrs_0.3.8              gtable_0.3.0            
 [85] purrr_0.3.4              amap_0.8-18              assertthat_0.2.1         cachem_1.0.6            
 [89] ashr_2.2-47              ggplot2_3.3.5            emdbook_1.3.12           xtable_1.8-4            
 [93] restfulr_0.0.13          coda_0.19-4              survival_3.2-13          truncnorm_1.0-8         
 [97] tibble_3.1.6             memoise_2.0.1            AnnotationDbi_1.56.2     GenomicAlignments_1.30.0
[101] ellipsis_0.3.2
BiocParallel BiocPa DiffBind • 378 views
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Entering edit mode

I have encountered exactly the same issue when I specified bParallel=FALSE for my ATAC-seq analysis. I have around 80000 peaks per sample (12 in total) and each BAM file is roughly 5 GB.

I read similar threads on this forum and tried out solutions such as adding the following parameters to dba.count() : summits=FALSE and bUseSummarizeOverlaps=TRUE but to no avail.

When I do not specify bParallel=FALSE, I get the following errors:

*Error: Error processing one or more read files. Check warnings().*
*In addition: There were 12 warnings (use warnings() to see them)*
> warnings() 
Warning messages: 
1: In mclapply(arglist, fn, ..., mc.preschedule = TRUE, mc.allow.recursive = TRUE) : 
  scheduled cores 2, 6, 3, 1, 5, 4, 10, 7, 9, 8, 12 encountered errors in user code, all values of the jobs will be affected 
2:   error in evaluating the argument 'x' in selecting a method for function 'assay': wrong args for environment subassignment 
3:   error in evaluating the argument 'x' in selecting a method for function 'assay': wrong args for environment subassignment 
4:   error in evaluating the argument 'x' in selecting a method for function 'assay': wrong args for environment subassignment 
5:   error in evaluating the argument 'x' in selecting a method for function 'assay': wrong args for environment subassignment 
6:   error in evaluating the argument 'x' in selecting a method for function 'assay': wrong args for environment subassignment 
7:   error in evaluating the argument 'x' in selecting a method for function 'assay': wrong args for environment subassignment 
8:   error in evaluating the argument 'x' in selecting a method for function 'assay': wrong args for environment subassignment 
9:   error in evaluating the argument 'x' in selecting a method for function 'assay': wrong args for environment subassignment 
10:   error in evaluating the argument 'x' in selecting a method for function 'assay': wrong args for environment subassignment 
11:   error in evaluating the argument 'x' in selecting a method for function 'assay': wrong args for environment subassignment 
12:   error in evaluating the argument 'x' in selecting a method for function 'assay': wrong args for environment subassignment*

Can any of these be caused by insufficient RAM? (My machine has 16 GB, DDR5).

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0
Entering edit mode
@b748553d
Last seen 11 weeks ago
United Kingdom

So, after I typed my comment, I tried one thing before loading the DiffBind library

> library(BiocParallel)
> register(SerialParam())

After that I ran

...
>counts <- dba.count(samples, bParallel=FALSE)

and it worked (but it still consumed like 8 GB of RAM per sample at a time).

Hope it helps!

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