error message

[bio-rain]

Hi, thanks for your help last time. I meet a error message like this: "Error in readAlleleCountFiles(tumourAlleleCountsFile.prefix, ".txt", chrom_names, : length(files) > 0 is not TRUE" and this is my input (in R):

ascat.prepareHTS(

• tumourseqfile = "ERR491757_Rsorted.bam",
• normalseqfile = "ERR491757_sorted.bam",
• tumourname = "hcc38R",
• normalname = "hcc38",
• allelecounter_exe = "~/allelecounter/bin/",
• alleles.prefix = "G1000_alleles_hg38_chr",
• loci.prefix = "G1000_loci_hg38_chr",
• gender = "XX",
• genomeVersion = "hg38",
• nthreads = 2,
• tumourLogR_file = "Tumor_LogR.txt",
• tumourBAF_file = "Tumor_BAF.txt",
• normalLogR_file = "Germline_LogR.txt",
• normalBAF_file = "Germline_BAF.txt") Error in readAlleleCountFiles(tumourAlleleCountsFile.prefix, ".txt", chrom_names, : length(files) > 0 is not TRUE I want to solve this problem, thank you

[tlesluyes]

Hi @bio-rain,

allelecounter_exe must be a path to the alleleCounter binary. In your script, it points to a folder so this needs to be fixed. Can you also check that G1000_alleles_hg38_chr and G1000_loci_hg38_chr (+ BAMs) are located in your working directory (or provide paths)?

Cheers,

Tom.

[bio-rain]

Hi, Tom Thank you for your answer My problem in "allelecounter_exe" has been solved But then there are new problems this is my input (in R): ascat.prepareHTS( tumourseqfile = "RM16-T.bam", normalseqfile = "RM16-N.bam", tumourname = "RM16-T", normalname = "RM16-N", allelecounter_exe = "~/allelecounter/bin/alleleCounter", alleles.prefix = "G1000_alleles_hg38_chr", loci.prefix = "G1000_loci_hg38_chr", gender = "XX", genomeVersion = "hg38", nthreads = 2, tumourLogR_file = "Tumor_LogR.txt", tumourBAF_file = "Tumor_BAF.txt", normalLogR_file = "Germline_LogR.txt", normalBAF_file = "Germline_BAF.txt") I check "G1000_alleles_hg38_chr" and "G1000_alleles_hg38_chr" in my folder (same as input) the error like this: Reading locis Reading locis Done reading locis Multi pos start: [E::sam_itr_next] Null iterator [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error detected (-2) when trying to iterate through region. [ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps. munmap_chunk(): invalid pointer Done reading locis Multi pos start: [E::sam_itr_next] Null iterator [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error detected (-2) when trying to iterate through region. [ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps. munmap_chunk(): invalid pointer Aborted (core dumped) Aborted (core dumped) Reading locis Reading locis Done reading locis then repeat above to the end

thanks a lot

bio-rain

[tlesluyes]

Hi @bio-rain,

Your last message is a combination of comments, code and log. Can you please use spacing and formatting to make it easier to read?

It seems like your issue is related to alleleCounter. If your BAM is located in your working directory, then my recommendation is to try running alleleCounter manually with one loci file. Is your BAM indexed? Do you have enough memory for the job to complete (12-18Gb)?

Cheers,

Tom.