There is a error when I using ASCAT analysis WES CNV.

Error in !is.null(homsegs) && !is.na(homsegs) : 'length = 3' in coercion to 'logical(1)' Calls: ascat.aspcf

` if (F){ ascat.prepareTargetedSeq( Worksheet = worksheet, # A tab-separated file with specific information. Check format using ?ascat.prepareTargetedSeq Workdir = output_dir, alleles.prefix = alleles_prefix, BED_file = bed_file, allelecounter_exe = allelecounter, genomeVersion = hg_version, is_chr_based=T, nthreads = 24) }

ascat.prepareHTS( tumourseqfile = tumor_bam, normalseqfile = normal_bam, tumourname = tumor_name, normalname = normal_name, allelecounter_exe = allelecounter, alleles.prefix = "./alleleData/Cleaned/alleleData_chr", loci.prefix = "./alleleData/Cleaned/loci_chr", gender = gender, genomeVersion = hg_version,

chrom_names = paste0('chr',c(1:22, "X")),

nthreads = 24, tumourLogR_file = paste0(tumor_name, "_LogR.txt"), tumourBAF_file = paste0(tumor_name, "_BAF.txt"), normalLogR_file = paste0(normal_name, "_LogR.txt"), normalBAF_file = paste0(normal_name, "_BAF.txt"))

print('======ascat.prepareHTS==========Finished.......')

ascat.bc = ascat.loadData(Tumor_LogR_file = paste0(tumor_name, "_LogR.txt"), Tumor_BAF_file = paste0(tumor_name, "_BAF.txt"), Germline_LogR_file = paste0(normal_name, "_LogR.txt"), Germline_BAF_file = paste0(normal_name, "_BAF.txt"), gender = gender, genomeVersion = hg_version, isTargetedSeq=T) print('=======ascat.bc======Finished.......')

ascat.plotRawData(ascat.bc, img.prefix = "Beforecorrection") ascat.bc = ascat.correctLogR(ascat.bc, GCcontentfile = gc_file, replictimingfile = rt_file) ascat.plotRawData(ascat.bc, img.prefix = "Aftercorrection") ascat.bc = ascat.aspcf(ascat.bc, penalty=25) ascat.plotSegmentedData(ascat.bc) ascat.output = ascat.runAscat(ascat.bc, gamma=1, write_segments = T) QC = ascat.metrics(ascat.bc,ascat.output) save(ascat.bc, ascat.output, QC, file =paste0(tumor_name,'ASCAT_objects.Rdata')) print('=======All======Finished.......') `

R version 4.3.1 (2023-06-16) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Ubuntu 20.04.6 LTS

Matrix products: default BLAS/LAPACK: /cpfs01/projects-HDD/cfff-e44ef5cf7aa5_HDD/dsm_23110700129/miniconda3/envs/ascat_env/lib/libopenblasp-r0.3.21.so; LAPACK version 3.9.0

locale: [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

time zone: Asia/Shanghai tzcode source: system (glibc)

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

loaded via a namespace (and not attached): [1] compiler_4.3.1

Package: ASCAT Type: Package Title: Allele-Specific Copy Number Analysis of Tumors Version: 3.1.1 Date: 2022-12-21 Authors@R: c(person("Peter", "Van Loo", role=c("aut","cre"), email="Peter.VanLoo@crick.ac.uk"), person("Gro", "Nielsen", role="ctb"), person("Jiqiu","Cheng", role="ctb"), person("Stefan","Dentro", role="ctb"), person("Edith","Ross", role="ctb"), person("Kerstin","Haase", role="ctb"), person("Jonas","Demeulemeester", role="ctb"), person("Maxime","Tarabichi", role="ctb"), person("Tom","Lesluyes", role="ctb")) Author: Peter Van Loo [aut, cre], Gro Nielsen [ctb], Jiqiu Cheng [ctb], Stefan Dentro [ctb], Edith Ross [ctb], Kerstin Haase [ctb], Jonas Demeulemeester [ctb], Maxime Tarabichi [ctb], Tom Lesluyes [ctb] Maintainer: Tom Lesluyes tom.lesluyes@crick.ac.uk Description: R package of ASCAT as published in http://www.ncbi.nlm.nih.gov/pubmed/20837533 Depends: R (>= 2.13.0), RColorBrewer, grDevices, graphics, stats, splines, data.table, GenomicRanges, IRanges, parallel, doParallel, foreach, utils License: GPL-3 Encoding: UTF-8 LazyLoad: yes RoxygenNote: 7.2.0 Built: R 4.3.1; ; 2023-07-14 02:30:43 UTC; unix

-- File: /cpfs01/projects-HDD/cfff-e44ef5cf7aa5_HDD/dsm_23110700129/miniconda3/envs/ascat_env/lib/R/library/ASCAT/Meta/package.rds

VanLoo-lab / ascat

Error in !is.null(homsegs) && !is.na(homsegs) #175

chrom_names = paste0('chr',c(1:22, "X")),