Error while running ChIPQC
1
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Entering edit mode
zebasilio • 0
@zebasilio-19655
Last seen 3.6 years ago

Hi!

I am trying to run ChiPQC and I am getting always an error message. Thank you for any help. best, José

**Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'which.max': NA/NaN argument**

The **traceback error**:

Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'which.max': NA/NaN argument
14.
h(simpleError(msg, call))
13.
.handleSimpleError(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)), "NA/NaN argument", base::quote(1:(2 * readlength(object))))
12.
seq(1:(2 * readlength(object)))
11.
running(crosscoverage(object)[-seq(1:(2 * readlength(object)))], width = width, allow.fewer = TRUE)
10.
which.max(running(crosscoverage(object)[-seq(1:(2 * readlength(object)))], width = width, allow.fewer = TRUE))
9.
FUN(X[[i]], ...)
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(samples, annotation = "hg19", blacklist = BlacklistFile, chromosomes = NULL)

My code is as follows:

chipseq = ChIPQC(samples, annotation="hg19", blacklist = BlacklistFile, chromosomes = NULL)

The sessionInfo:

R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] goseq_1.40.0                            geneLenDataBase_1.24.0                  BiasedUrn_1.07                         
 [4] KEGG.db_3.2.4                           ChIPseeker_1.24.0                       TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [7] GenomicFeatures_1.40.1                  ChIPQC_1.24.1                           DiffBind_2.16.0                        
[10] BiocStyle_2.16.1                        systemPipeRdata_1.16.2                  runner_0.3.7                           
[13] plotly_4.9.2.1                          analyze.stuff_1.0.0                     dplyr_1.0.2                            
[16] lubridate_1.7.9                         tidyr_1.1.2                             openxlsx_4.2.3                         
[19] data.table_1.13.2                       clusterProfiler_3.17.1                  pheatmap_1.0.12                        
[22] transcripTools_0.0.0.9000               kableExtra_1.3.1                        knitr_1.30                             
[25] org.Hs.eg.db_3.11.4                     AnnotationDbi_1.50.3                    ReactomePA_1.32.0                      
[28] edgeR_3.30.3                            batchtools_0.9.14                       ape_5.4-1                              
[31] ggplot2_3.3.2                           systemPipeR_1.22.0                      ShortRead_1.46.0                       
[34] GenomicAlignments_1.24.0                SummarizedExperiment_1.18.2             DelayedArray_0.14.1                    
[37] matrixStats_0.57.0                      Biobase_2.48.0                          BiocParallel_1.22.0                    
[40] Rsamtools_2.4.0                         Biostrings_2.56.0                       XVector_0.28.0                         
[43] GenomicRanges_1.40.0                    GenomeInfoDb_1.24.2                     IRanges_2.22.2                         
[46] S4Vectors_0.26.1                        BiocGenerics_0.34.0                     limma_3.44.3                           

loaded via a namespace (and not attached):
  [1] statnet.common_4.4.1                      Hmisc_4.4-1                               ps_1.4.0                                 
  [4] rsvg_2.1                                  foreach_1.5.1                             rprojroot_1.3-2                          
  [7] crayon_1.3.4                              V8_3.3.1                                  MASS_7.3-53                              
 [10] nlme_3.1-150                              backports_1.1.10                          impute_1.62.0                            
 [13] GOSemSim_2.14.2                           MeSHDbi_1.24.0                            rlang_0.4.8                              
 [16] intergraph_2.0-2                          callr_3.5.1                               GOstats_2.54.0                           
 [19] rjson_0.2.20                              chipseq_1.38.0                            CEMiTool_1.12.2                          
 [22] bit64_4.0.5                               glue_1.4.2                                processx_3.4.4                           
 [25] base64url_1.4                             DOSE_3.15.1                               tidyselect_1.1.0                         
 [28] usethis_1.6.3                             XML_3.99-0.5                              xtable_1.8-4                             
 [31] magrittr_1.5                              evaluate_0.14                             cli_2.1.0                                
 [34] zlibbioc_1.34.0                           hwriter_1.3.2                             rstudioapi_0.11                          
 [37] rpart_4.1-15                              fastmatch_1.1-0                           xfun_0.19                                
 [40] askpass_1.1                               pkgbuild_1.1.0                            cluster_2.1.0                            
 [43] caTools_1.18.0                            tidygraph_1.2.0                           tibble_3.0.4                             
 [46] ggrepel_0.8.2                             png_0.1-7                                 withr_2.3.0                              
 [49] rle_0.9.2                                 bitops_1.0-6                              ggforce_0.3.2                            
 [52] RBGL_1.64.0                               plyr_1.8.6                                GSEABase_1.50.1                          
 [55] pracma_2.2.9                              coda_0.19-4                               pillar_1.4.6                             
 [58] gplots_3.1.0                              TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 fs_1.5.0                                 
 [61] graphite_1.34.0                           europepmc_0.4                             vctrs_0.3.4                              
 [64] ellipsis_0.3.1                            generics_0.1.0                            urltools_1.7.3                           
 [67] devtools_2.3.2                            tools_4.0.3                               foreign_0.8-80                           
 [70] munsell_0.5.0                             tweenr_1.0.1                              fgsea_1.14.0                             
 [73] compiler_4.0.3                            pkgload_1.1.0                             rtracklayer_1.48.0                       
 [76] sessioninfo_1.1.1                         GenomeInfoDbData_1.2.3                    gridExtra_2.3                            
 [79] lattice_0.20-41                           AnnotationForge_1.30.1                    BiocFileCache_1.12.1                     
 [82] jsonlite_1.7.1                            scales_1.1.1                              TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2  
 [85] graph_1.66.0                              genefilter_1.70.0                         lazyeval_0.2.2                           
 [88] MeSH.db_1.13.0                            doParallel_1.0.16                         latticeExtra_0.6-29                      
 [91] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2   brew_1.0-6                                sna_2.6                                  
 [94] checkmate_2.0.0                           rmarkdown_2.5                             cowplot_1.1.0                            
 [97] webshot_0.5.2                             downloader_0.4                            BSgenome_1.56.0                          
[100] igraph_1.2.6                              survival_3.2-7                            rsconnect_0.8.16                         
[103] yaml_2.2.1                                plotrix_3.7-8                             htmltools_0.5.0                          
[106] memoise_1.1.0                             VariantAnnotation_1.34.0                  locfit_1.5-9.4                           
[109] graphlayouts_0.7.1                        viridisLite_0.3.0                         digest_0.6.27                            
[112] assertthat_0.2.1                          rappdirs_0.3.1                            RSQLite_2.2.1                            
[115] amap_0.8-18                               remotes_2.2.0                             blob_1.2.1                               
[118] preprocessCore_1.50.0                     splines_4.0.3                             Formula_1.2-4                            
[121] labeling_0.4.2                            RCurl_1.98-1.2                            hms_0.5.3                                
[124] colorspace_1.4-1                          base64enc_0.1-3                           BiocManager_1.30.10                      
[127] nnet_7.3-14                               Rcpp_1.0.5                                enrichplot_1.8.1                         
[130] fansi_0.4.1                               Nozzle.R1_1.1-1                           R6_2.5.0                                 
[133] grid_4.0.3                                ggridges_0.5.2                            lifecycle_0.2.0                          
[136] zip_2.1.1                                 curl_4.3                                  TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2  
[139] testthat_3.0.0                            fastcluster_1.1.25                        DO.db_2.9                                
[142] Matrix_1.2-18                             TxDb.Celegans.UCSC.ce6.ensGene_3.2.2      qvalue_2.20.0                            
[145] desc_1.2.0                                RColorBrewer_1.1-2                        iterators_1.0.13                         
[148] stringr_1.4.0                             DOT_0.1                                   htmlwidgets_1.5.2                        
[151] polyclip_1.10-0                           triebeard_0.3.0                           biomaRt_2.44.1                           
[154] purrr_0.3.4                               network_1.16.1                            gridGraphics_0.5-0                       
[157] reactome.db_1.70.0                        mgcv_1.8-33                               rvest_0.3.6                              
[160] openssl_1.4.3                             htmlTable_2.1.0                           codetools_0.2-16                         
[163] GO.db_3.11.4                              gtools_3.8.2                              prettyunits_1.1.1                        
[166] dbplyr_1.4.4                              gtable_0.3.0                              DBI_1.1.0                                
[169] ggpmisc_0.3.6                             dynamicTreeCut_1.63-1                     httr_1.4.2                               
[172] KernSmooth_2.23-18                        stringi_1.5.3                             progress_1.2.2                           
[175] reshape2_1.4.4                            farver_2.0.3                              annotate_1.66.0                          
[178] viridis_0.5.1                             ggthemes_4.2.0                            Rgraphviz_2.32.0                         
[181] DT_0.16                                   xml2_1.3.2                                ggdendro_0.1.22                          
[184] rvcheck_0.1.8                             boot_1.3-25                               WGCNA_1.69                               
[187] ggplotify_0.0.5                           Category_2.54.0                           bit_4.0.4                                
[190] scatterpie_0.1.5                          jpeg_0.1-8.1                              TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0
[193] ggraph_2.0.3                              pkgconfig_2.0.3                           meshes_1.14.0   
ChIPQC • 1.5k views
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0
Entering edit mode
zebasilio • 0
@zebasilio-19655
Last seen 3.6 years ago

Hi!

I added the chromossomes as a vector and it worked, no error message.

x = c(paste0("chr",seq(1:22)), "chrY","chrX")
chipseq = ChIPQC(samples, annotation="hg19", blacklist = BlacklistFile, chromosomes = x)
ADD COMMENT
0
Entering edit mode

Thank you for posting the answer. Out of curiosity, you have an excessive amount of packages loaded - do you need all of these? It's good practice to close your session and then restart it for every analysis.

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