Hello I hope you are doing well; I am running into this issue when I am trying to run dba.count().

This is the code I am using:

#Create a new DBA object using the subset data
myDBA <- dba(sampleSheet = subset_data)
myDBA <- dba.count(myDBA, bUseSummarizeOverlaps=FALSE)
print(myDBA)

It does the following: Computing summits... Re-centering peaks... Reads will be counted as Paired-end. Error: No sites have activity greater than filter value.

However I also tried to do the following:

myDBA <- dba.count(myDBA, bUseSummarizeOverlaps=FALSE)
print(myDBA)

But I get the same error

Re-centering peaks... Error: No sites have activity greater than filter value.

Any ideas on what this error is indicating or how I can fix it?

Code should be placed in three backticks as shown below

sessionInfo( )
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /hpc/packages/minerva-centos7/intel/parallel_studio_xe_2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.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] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] reshape2_1.4.4              ggpubr_0.4.0               
 [3] ggplot2_3.4.1               DESeq2_1.36.0              
 [5] DiffBind_3.6.3              SummarizedExperiment_1.26.1
 [7] Biobase_2.56.0              MatrixGenerics_1.8.1       
 [9] matrixStats_0.62.0          GenomicRanges_1.48.0       
[11] GenomeInfoDb_1.34.9         IRanges_2.30.0             
[13] S4Vectors_0.34.0            BiocGenerics_0.42.0        

loaded via a namespace (and not attached):
  [1] amap_0.8-18              colorspace_2.0-3         ggsignif_0.6.3          
  [4] rjson_0.2.21             hwriter_1.3.2.1          XVector_0.36.0          
  [7] ggrepel_0.9.1            bit64_4.0.5              AnnotationDbi_1.58.0    
 [10] fansi_1.0.3              mvtnorm_1.1-3            apeglm_1.18.0           
 [13] codetools_0.2-18         splines_4.2.0            cachem_1.0.6            
 [16] geneplotter_1.74.0       Rsamtools_2.12.0         broom_1.0.5             
 [19] annotate_1.74.0          ashr_2.2-54              png_0.1-7               
 [22] GreyListChIP_1.28.1      compiler_4.2.0           httr_1.4.3              
 [25] backports_1.4.1          Matrix_1.5-1             fastmap_1.1.0           
 [28] limma_3.52.4             cli_3.6.1                htmltools_0.5.5         
 [31] tools_4.2.0              coda_0.19-4              gtable_0.3.0            
 [34] glue_1.6.2               GenomeInfoDbData_1.2.8   systemPipeR_2.2.2       
 [37] dplyr_1.1.2              ShortRead_1.54.0         Rcpp_1.0.10             
 [40] carData_3.0-5            bbmle_1.0.25             vctrs_0.6.3             
 [43] Biostrings_2.64.0        rtracklayer_1.56.1       stringr_1.4.0           
 [46] lifecycle_1.0.3          irlba_2.3.5              restfulr_0.0.15         
 [49] gtools_3.9.2.2           rstatix_0.7.0            XML_3.99-0.10           
 [52] zlibbioc_1.42.0          MASS_7.3-56              scales_1.2.1            
 [55] BSgenome_1.64.0          parallel_4.2.0           RColorBrewer_1.1-3      
 [58] yaml_2.3.5               memoise_2.0.1            emdbook_1.3.12          
 [61] bdsmatrix_1.3-6          latticeExtra_0.6-29      stringi_1.7.6           
 [64] RSQLite_2.2.14           SQUAREM_2021.1           genefilter_1.78.0       
 [67] BiocIO_1.6.0             caTools_1.18.2           BiocParallel_1.30.3     
 [70] truncnorm_1.0-8          rlang_1.1.1              pkgconfig_2.0.3         
 [73] bitops_1.0-7             lattice_0.20-45          invgamma_1.1            
 [76] purrr_1.0.1              GenomicAlignments_1.32.0 htmlwidgets_1.6.2       
 [79] bit_4.0.4                tidyselect_1.2.0         plyr_1.8.7              
 [82] magrittr_2.0.3           R6_2.5.1                 gplots_3.1.3            
 [85] generics_0.1.2           DelayedArray_0.22.0      DBI_1.1.3               
 [88] pillar_1.9.0             withr_2.5.0              abind_1.4-5             
 [91] survival_3.3-1           KEGGREST_1.36.2          RCurl_1.98-1.7          
 [94] mixsqp_0.3-43            tibble_3.2.1             crayon_1.5.1            
 [97] car_3.1-0                KernSmooth_2.23-20       utf8_1.2.3              
[100] jpeg_0.1-9               locfit_1.5-9.5           grid_4.2.0              
[103] blob_1.2.3               digest_0.6.29            xtable_1.8-4            
[106] tidyr_1.2.0              numDeriv_2016.8-1.1      munsell_0.5.0

same problem! any solution?