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

[duanshumeng]

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 = "Before_correction_")
ascat.bc = ascat.correctLogR(ascat.bc, GCcontentfile = gc_file, replictimingfile = rt_file)
ascat.plotRawData(ascat.bc, img.prefix = "After_correction_")
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

[zhangzhhcb]

IIt may be due to the version of R. Please refer to this poster. #166. If it is not the case, I may need more details of your issue.