Received the exact same error, when running on ChIPQC 1.4.3.

I have not, however, run my data on any other version.

Any suggestions?

> ExperimentFile<-"/home/khoegenauer/Data/Analysis/HSC_Lineage_ChIP-seq/H3K27ac/H3K27ac_1_2_MACS2.csv"
> BlacklistFile<-"/media/Data/Genome/Mouse/mm9/Features/ENCODE_ChIP-seq_Blacklist/mm9-blacklist.bed"
> expQC = ChIPQC(experiment=ExperimentFile, annotation="mm9", blacklist=BlacklistFile, chromosomes = NULL)
GMP_MACS2_1 GMP H3K27ac  MACS2 1 “bed”
GMP_MACS2_2 GMP H3K27ac  MACS2 2 “bed”
GMP_MACS2_IDR GMP H3K27ac  MACS2-IDR 1 “bed”
HSC_MACS2_1 HSC H3K27ac  MACS2 1 “bed”
HSC_MACS2_2 HSC H3K27ac  MACS2 2 “bed”
HSC_MACS2_IDR HSC H3K27ac  MACS2-IDR 1 “bed”
MPP_MACS2_1 MPP H3K27ac  MACS2 1 “bed”
MPP_MACS2_IDR MPP H3K27ac  MACS2-IDR 1 “bed”
WBM_MACS2_1 WBM H3K27ac  MACS2 1 “bed”
WBM_MACS2_2 WBM H3K27ac  MACS2 2 “bed”
WBM_MACS2_IDR WBM H3K27ac  MACS2-IDR 1 “bed”
Compiling annotation...
Computing metrics for 22 samples...
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘fragmentlength’ for signature ‘"remote-error"’

> traceback()
10: stop(gettextf("unable to find an inherited method for function %s for signature %s",
        sQuote(fdef@generic), sQuote(cnames)), domain = NA)
9: (function (classes, fdef, mtable)
   {
       methods <- .findInheritedMethods(classes, fdef, mtable)
       if (length(methods) == 1L)
           return(methods[[1L]])
       else if (length(methods) == 0L) {
           cnames <- paste0("\"", vapply(classes, as.character,
               ""), "\"", collapse = ", ")
           stop(gettextf("unable to find an inherited method for function %s for signature %s",
               sQuote(fdef@generic), sQuote(cnames)), domain = NA)
       }
       else stop("Internal error in finding inherited methods; didn't return a unique method",
           domain = NA)
   })(list("remote-error"), function (object = "ChIPQCsample", width)
   standardGeneric("fragmentlength"), <environment>)
8: FUN(X[[i]], ...)
7: lapply(X = X, FUN = FUN, ...)
6: sapply(object@Samples, fragmentlength)
5: sapply(object@Samples, fragmentlength)
4: .local(object)
3: fragmentlength(res)
2: fragmentlength(res)
1: ChIPQC(experiment = ExperimentFile, annotation = "mm9", blacklist = BlacklistFile,
       chromosomes = NULL)

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8      
 [2] LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8      
 [8] LC_NAME=C                 
 [9] LC_ADDRESS=C              
[10] LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8
[12] LC_IDENTIFICATION=C       

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

other attached packages:
 [1] ChIPQC_1.4.3                           
 [2] DiffBind_1.14.3                        
 [3] RSQLite_1.0.0                          
 [4] DBI_0.3.1                              
 [5] locfit_1.5-9.1                         
 [6] GenomicAlignments_1.4.1                
 [7] Rsamtools_1.20.2                       
 [8] Biostrings_2.36.1                      
 [9] XVector_0.8.0                          
[10] limma_3.24.4                           
[11] ggplot2_1.0.1                          
[12] TxDb.Mmusculus.UCSC.mm9.knownGene_3.1.2
[13] GenomicFeatures_1.20.1                 
[14] BiocInstaller_1.18.2                   
[15] AnnotationDbi_1.30.1                   
[16] Biobase_2.28.0                         
[17] GenomicRanges_1.20.3                   
[18] GenomeInfoDb_1.4.0                     
[19] IRanges_2.2.1                          
[20] S4Vectors_0.6.0                        
[21] BiocGenerics_0.14.0                    

loaded via a namespace (and not attached):
 [1] edgeR_3.10.0          
 [2] splines_3.2.0         
 [3] gtools_3.4.2          
 [4] latticeExtra_0.6-26   
 [5] amap_0.8-14           
 [6] RBGL_1.44.0           
 [7] BSgenome_1.36.0       
 [8] Category_2.34.2       
 [9] lattice_0.20-31       
[10] digest_0.6.8          
[11] RColorBrewer_1.1-2    
[12] checkmate_1.5.3       
[13] colorspace_1.2-6      
[14] Matrix_1.2-0          
[15] plyr_1.8.2            
[16] GSEABase_1.30.1       
[17] chipseq_1.18.0        
[18] XML_3.98-1.1          
[19] pheatmap_1.0.2        
[20] ShortRead_1.26.0      
[21] biomaRt_2.24.0        
[22] genefilter_1.50.0     
[23] zlibbioc_1.14.0       
[24] xtable_1.7-4          
[25] GO.db_3.1.2           
[26] scales_0.2.4          
[27] snow_0.3-13           
[28] brew_1.0-6            
[29] gdata_2.16.1          
[30] BiocParallel_1.2.1    
[31] annotate_1.46.0       
[32] proto_0.3-10          
[33] survival_2.38-1       
[34] magrittr_1.5          
[35] systemPipeR_1.2.1     
[36] fail_1.2              
[37] MASS_7.3-40           
[38] gplots_2.17.0         
[39] hwriter_1.3.2         
[40] GOstats_2.34.0        
[41] graph_1.46.0          
[42] tools_3.2.0           
[43] BBmisc_1.9            
[44] stringr_1.0.0         
[45] sendmailR_1.2-1       
[46] munsell_0.4.2         
[47] lambda.r_1.1.7        
[48] caTools_1.17.1        
[49] futile.logger_1.4.1   
[50] grid_3.2.0            
[51] RCurl_1.95-4.6        
[52] rjson_0.2.15          
[53] AnnotationForge_1.10.1
[54] bitops_1.0-6          
[55] base64enc_0.1-2       
[56] gtable_0.1.2          
[57] reshape2_1.4.1        
[58] Nozzle.R1_1.1-1       
[59] rtracklayer_1.28.2    
[60] futile.options_1.0.0  
[61] KernSmooth_2.23-14    
[62] stringi_0.4-1         
[63] BatchJobs_1.6         
[64] Rcpp_0.11.6           

mm9 blacklist file was obtained from ENCODE.

Reads are from Ion Torrent (Proton), if that makes a difference.

Peaks are narrowPeak files from MACS v2.1 (Received the same error after running with peaks from HOMER v4.7 converted to narrowPeak format.)

Thanks.

Ran again and received this:

Error in sample TEST1: error in evaluating the argument 'x' in selecting a method for function 'mean': Error in width(temp[1:tocheckforreads]) :
  error in evaluating the argument 'x' in selecting a method for function 'width': Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
  subscript contains NAs or out-of-bounds indices

I filtered out any chromosome containing <1000 mapped reads (1000 = value of tocheckforreads) -- Mt, in my case -- and ran again. When returning to this stage, no error.

Later, i received:

Error in which.max(running(crosscoverage(object)[-seq(1:(2 * readlength(object)))],  :
  error in evaluating the argument 'x' in selecting a method for function 'which.max': Error in 1:(2 * readlength(object)) : NA/NaN argument

Running each sample individually (as well as subsetting each sample to any one chromosome) via ChIPQCsample revealed that readlength is not being set for any of the samples.

As individual ChIPQCsample objects, the error isn't apparent until inspecting the object. When running ChIPQC, however, the error terminates execution.

With limited background knowledge on objects in R, https://github.com/Bioconductor-mirror/ChIPQC/blob/master/R/ChIPQCsample-class.R#L80 didn't give me any leads.

Suggestions?

Thanks,

Kevin