Error in readAllelesFiles(alleles.prefix, ".txt", chrom_names) : length(files) > 0 is not TRUE

[fiviviani]

Hi,
I'm sorry to bother, but I was not able to find the solution in the previous issues and I don't know how to fix the issue because all the files seem fine.

I'm running ascat.prepareHTS on both tumor and normal WGS samples, I dowloaded the reference files (alleles and loci files for hg38 + Tumor/Germline_LogR/BAF) and added the "chr" prexif as needed for my BAM files.

So, I ran

ascat.prepareHTS(
tumourseqfile = "/wgs/bam_CNV/WGS/ID148-T.final.bam",
normalseqfile = "/wgs/bam_CNV/WGS/ID148-N.final.bam",
tumourname = "ID148-T",
normalname = "ID148-N",
allelecounter_exe = "/utilities/genomic_tools_fv/bin/alleleCounter",
alleles.prefix = "/wgs/ASCAT/G1000_alleles_WGS_hg38/G1000_alleles_hg38",
loci.prefix = "/wgs/ASCAT/G1000_loci_WGS_hg38/G1000_loci_hg38_chr",
gender = "XY",
genomeVersion = "hg38",
nthreads = 18,
tumourLogR_file = "/wgs/ASCAT/Tumor_LogR.txt",
tumourBAF_file = "/wgs/ASCAT/Tumor_BAF.txt",
normalLogR_file = "/wgs/ASCAT/Germline_LogR.txt",
normalBAF_file = "/wgs/ASCAT/Germline_BAF.txt")

This is the output

[W::hts_idx_load3] The index file is older than the data file: /wgs/bam_CNV/WGS/ID148-T.final.bam.bai
Reading locis
Reading locis
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Done reading locis
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Done reading locis
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Done reading locis
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Done reading locis
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Error in readAllelesFiles(alleles.prefix, ".txt", chrom_names) :
length(files) > 0 is not TRUE

But the alleleFrequencies files seem to have been correctly created

• ID148-N_alleleFrequencies_chr1
  #CHR POS Count_A Count_C Count_G Count_T Good_depth
  chr1 809641 0 0 20 11 31
  chr1 812761 3 0 16 0 19
  chr1 817186 16 0 15 0 31
  chr1 818954 0 17 0 14 31
  chr1 825532 0 11 0 21 32

• ID148-T_alleleFrequencies_chr1
  #CHR POS Count_A Count_C Count_G Count_T Good_depth
  chr1 809641 0 0 35 24 59
  chr1 812761 12 0 33 0 45
  chr1 817186 26 0 42 0 68
  chr1 818954 0 33 0 34 67
  chr1 825532 0 41 0 39 80

Would you please help me?
Thank you in advance.

[MonikaCho]

Hello ascat developers,

Thank you for creating and up-keeping this tool. It's truly fantastic to use and I've used it in the past. However, now re-setting up this tool on a new computing network and specifically running the ascat.prepareHTS command, I am receiving a similar error to the user above.

Error in readAlleleCountFiles(tumourAlleleCountsFile.prefix, ".txt", chrom_names, :
length(files) > 0 is not TRUE

I have run allelecounts outside of this function and successfully obtained counts, verifying that the executable works, as well as the allele reference file being correctly formatted. I have verified the correct file paths, which I've hard coded into the executable script. The above error pops up when running within the ascat conda environment. No intermediary files are created.

Additionally, as a test, do you provide small sample bams to verify the correct setup of this tool in using this function specifically?

Thank you in advance,
Monika C

[MonikaCho]

As things go, I was able to resolve this issue not long after posting, at least for my error after finding this thread here: https://www.biostars.org/p/9492757/

It explains the

alleles.prefix = "/G1000_alleles_WGS_hg38/G1000_alleles_hg38",
loci.prefix = "/G1000_loci_WGS_hg38/G1000_loci_hg38_chr",

are not simply path parameters. The R script looks for the specific prefix of each loci and allele txt file within the reference directories. Therefore, it is essential for both paths to contain the whole prefix:

alleles.prefix = "/G1000_alleles_WGS_hg38/G1000_alleles_hg38_chr",
loci.prefix = "/G1000_loci_WGS_hg38/G1000_loci_hg38_chr",

After updating these in my script, the run was successful. I do recall the instructions directing to set the prefixes to G1000_loci_hg19_chr and G1000_alleles_hg19_chr, however waved this off thinking it was local path specific. https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS

Hope this was helpful,
Monika C

[fiviviani]

Thank you so much, Monika!
After studying the code of the function, I started to suspect that writing the full path might have caused the error, and your comment confirmed it. I was able to successfully run the function today.
Thanks again.
All the best,
Filippo