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zebasilio
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@zebasilio-19655
Last seen 3.4 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
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.