Error in function make_segments

Hello! I'am running the module ASCAT from nextflow and I have the following error:

Warning messages:
1: In !is.null(homsegs) && !is.na(homsegs) :
  'length(x) = 3 > 1' in coercion to 'logical(1)'
2: In !is.null(homsegs) && !is.na(homsegs) :
  'length(x) = 3 > 1' in coercion to 'logical(1)'
[1] Sample test_tumor_T1_vs_test_normal_T1.tumour (1/1)
Error in m[i, 2] : subscript out of bounds
Calls: ascat.runAscat -> runASCAT -> make_segments
Execution halted

So I checked the output of the function that segment the data:

#Segment the data
ascat.bc = ascat.aspcf(ascat.bc, seed=42)
print(ascat.bc$Tumor_LogR_segmented)

            test_tumor_T1_vs_test_normal_T1.tumour
21_14221174                              0.5881753
21_14582339                              0.5881753
21_25587877                             -0.1100367
...

print(ascat.bc$Tumor_BAF_segmented)

[[1]]
     [,1]

The length for the ascat.bc$Tumor_LogR_segmented is 59 (I don't know if this result is the expected one or not) and obviously something is wrong with the output ascat.bc$Tumor_BAF_segmented because it only has one value. Does anyone know what this could be due to?

Also, I add here the commands that have been used as input:

#build prefixes: <abspath_to_files/prefix_chr>
allele_path = normalizePath("G1000_alleles_hg38")
allele_prefix = paste0(allele_path, "/", "G1000_alleles_hg38", "_chr")

loci_path = normalizePath("G1000_loci_hg38_chr")
loci_prefix = paste0(loci_path, "/", "G1000_loci_hg38_chr", "_chr")

#prepare from BAM files
ascat.prepareHTS(
    tumourseqfile = "test_tumor_T1.sorted.bam",
    normalseqfile = "test_normal_T1.sorted.bam",
    tumourname = paste0("test_tumor_T1_vs_test_normal_T1", ".tumour"),
    normalname = paste0("test_tumor_T1_vs_test_normal_T1", ".normal"),
    allelecounter_exe = "alleleCounter",
    alleles.prefix = allele_prefix,
    loci.prefix = loci_prefix,
    gender = "XX",
    genomeVersion = "hg38",
    nthreads = 6

    ,chrom_names = c(1:22, 'X')

    ,
    seed = 42
)

Thank you in advance,

Ana

VanLoo-lab / ascat

Error in function make_segments #171