Error in the first step

[beginner984]

Hi

I have tumour only (WGS), from human cell line (24x)

I get this error

> res <- run_targeted_sequencing(tumour_bams=".recal.bam", #full paths to your BAMs
                               bed_file=NULL, #your bed file definition of the targets
                               sex="female",#sex of bam's patient
                               chrstring_bam="chr",#string for contig names
                               allchr=paste0("chr",c(1:22,"X", "Y")),#contig names
                                                           build="hg38", #build 
                               normal_bams=NULL) #path to normal_bams 
[1] "## load bins for genome build"
[1] "## read in bed file"
Error in read.table(bed_file, sep = "\t", header = F) : 
  'file' must be a character string or connection

> res <- run_targeted_sequencing(tumour_bams="/fastq/preprocessing/recalibrated/recal.recal.bam", #full paths to your BAMs
                               bed_file=NULL, #your bed file definition of the targets
                               sex="female",#sex of bam's patient
                               chrstring_bam="chr",#string for contig names
                               allchr=paste0("chr",c(1:22,"X", "Y")),#contig names
                                                           build="hg38", #build 
                               normal_bams=NULL) #path to normal_bams 
[1] "## load bins for genome build"
[1] "## read in bed file"
Error in read.table(bed_file, sep = "\t", header = F) : 
  'file' must be a character string or connection
> 

Please could you help me with this error

> sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Rocky Linux 8.7 (Green Obsidian)

Matrix products: default
BLAS/LAPACK: FlexiBLAS OPENBLAS;  LAPACK version 3.11.0

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

time zone: Europe/London
tzcode source: system (glibc)

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

other attached packages:
 [1] copynumber_1.29.0.9000 DNAcopy_1.78.0         Rsamtools_2.20.0      
 [4] Biostrings_2.72.1      XVector_0.44.0         ASCAT.sc_0.1          
 [7] ASCAT_3.1.2            doParallel_1.0.17      iterators_1.0.14      
[10] foreach_1.5.2          GenomicRanges_1.56.2   GenomeInfoDb_1.40.1   
[13] IRanges_2.38.1         S4Vectors_0.42.1       BiocGenerics_0.50.0   
[16] data.table_1.16.2      RColorBrewer_1.1-3    

loaded via a namespace (and not attached):
 [1] bitops_1.0-9            digest_0.6.37           magrittr_2.0.3         
 [4] pkgload_1.4.0           fastmap_1.2.0           jsonlite_1.8.9         
 [7] processx_3.8.4          pkgbuild_1.4.4          sessioninfo_1.2.2      
[10] BiocManager_1.30.25     ps_1.8.0                urlchecker_1.0.1       
[13] promises_1.3.0          httr_1.4.7              purrr_1.0.2            
[16] UCSC.utils_1.0.0        codetools_0.2-20        cli_3.6.3              
[19] shiny_1.9.1             crayon_1.5.3            rlang_1.1.4            
[22] ellipsis_0.3.2          remotes_2.5.0           cachem_1.1.0           
[25] devtools_2.4.5          tools_4.4.0             BiocParallel_1.38.0    
[28] memoise_2.0.1           httpuv_1.6.15           GenomeInfoDbData_1.2.12
[31] curl_5.2.3              vctrs_0.6.5             R6_2.5.1               
[34] mime_0.12               lifecycle_1.0.4         zlibbioc_1.50.0        
[37] fs_1.6.4                htmlwidgets_1.6.4       usethis_3.0.0          
[40] miniUI_0.1.1.1          callr_3.7.6             desc_1.4.3             
[43] later_1.3.2             glue_1.8.0              profvis_0.4.0          
[46] Rcpp_1.0.13             xtable_1.8-4            htmltools_0.5.8.1      
[49] compiler_4.4.0         
> 

[galder-max]

Dear @beginner984, thanks for using ASCAT.sc. Please have a look at the Wiki pages. For WGS, the function run_sc_sequencing should be run. Please also make sure to feed the proper human build for your data (hg19 or hg38) in the input parameters.

The function run_targeted_sequencing is for targeted sequencing (such as exome or targeted panels) and thus requires a bed file as input, which you do not have/need.