Closed teodorabu closed 1 year ago
Hi @teodorabu,
This seems linked to an issue with alleleCounter rather than an issue with ASCAT. Did you have sufficient memory when running ascat.prepareHTS
? It'll parallelise the alleleCounter step (on threads per chromosome) and use nthreads
, maybe it ran out of memory. Or you can try setting a lower number of threads.
It's a bit weird that you only get 0s in the output, do you have other values and/or is "1" the real chromosome name or is it "chr1"?
Cheers,
Tom.
Hi, the issue was with the index files. It works now, thanks!
Hi, I have been using Ascat for a while now on multiple matched normal-tumor samples, but somehow with new data that I need to analyze I am getting the following error message when running the fuction ascat.prepareHTS:
ascat.prepareHTS( tumourseqfile=paste0(test_folder, args[1]), normalseqfile=paste0(test_folder,args[3]), tumourname = paste0(tumor_accession,"_tumour"), normalname = paste0(tumor_accession, "_normal"), allelecounter_exe = "alleleCounter", alleles.prefix= ref_alleles, loci.prefix = ref_loci, tumourLogR_file = paste0(tumor_accession, "_tumour.LogR.tsv"), tumourBAF_file = paste0(tumor_accession, "_tumour.BAF.tsv"), normalLogR_file = paste0(normalaccession,"",tumor_accession, "_normal.LogR.tsv"), normalBAF_file = paste0(normalaccession,"", tumor_accession, "_normal.BAF.tsv"), gender = args[8], genomeVersion = args[9], chrom_names = c(1:22), nthreads= args[10], min_base_qual = 20, min_map_qual = 35, minCounts=10)
Error message: 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.
The loci and allele file are provided with the global path. I ran from the commandline "alleleCounter -l loci_file_hg19_mod.txt -b DRR003_BL.bam -o drr03_test.out --dense-snps -m 20 -q 35 -d" and I got the expected output, from which I attach a few lines: #CHR POS Count_A Count_C Count_G Count_T Good_depth 1 751343 0 0 0 0 0 1 753425 0 0 0 0 0 1 755940 0 0 0 0 0 1 756257 0 0 0 0 0 1 756268 0 0 0 0 0 1 756378 0 0 0 0 0 1 756380 0 0 0 0 0 1 762601 0 0 0 0 0 1 764191 0 0 0 0 0 1 768253 0 0 0 0 0 1 768448 0 0 0 0 0 1 772755 0 0 0 0 0 1 775659 0 0 0 0 0
Could you maybe help me solve this issue? Cheers, Teodora
Hello, I was wondering how you handle column names for loci files? Should it correspond to something in the bam file?In my file, there are only two columns
Hi, I have been using Ascat for a while now on multiple matched normal-tumor samples, but somehow with new data that I need to analyze I am getting the following error message when running the fuction ascat.prepareHTS:
ascat.prepareHTS( tumourseqfile=paste0(test_folder, args[1]), normalseqfile=paste0(test_folder,args[3]), tumourname = paste0(tumor_accession,"_tumour"), normalname = paste0(tumor_accession, "_normal"), allelecounter_exe = "alleleCounter", alleles.prefix= ref_alleles, loci.prefix = ref_loci, tumourLogR_file = paste0(tumor_accession, "_tumour.LogR.tsv"), tumourBAF_file = paste0(tumor_accession, "_tumour.BAF.tsv"), normalLogR_file = paste0(normalaccession,"",tumor_accession, "_normal.LogR.tsv"), normalBAF_file = paste0(normalaccession,"", tumor_accession, "_normal.BAF.tsv"), gender = args[8], genomeVersion = args[9], chrom_names = c(1:22), nthreads= args[10], min_base_qual = 20, min_map_qual = 35, minCounts=10)
Error message: 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.
The loci and allele file are provided with the global path. I ran from the commandline "alleleCounter -l loci_file_hg19_mod.txt -b DRR003_BL.bam -o drr03_test.out --dense-snps -m 20 -q 35 -d" and I got the expected output, from which I attach a few lines:
CHR POS Count_A Count_C Count_G Count_T Good_depth
1 751343 0 0 0 0 0 1 753425 0 0 0 0 0 1 755940 0 0 0 0 0 1 756257 0 0 0 0 0 1 756268 0 0 0 0 0 1 756378 0 0 0 0 0 1 756380 0 0 0 0 0 1 762601 0 0 0 0 0 1 764191 0 0 0 0 0 1 768253 0 0 0 0 0 1 768448 0 0 0 0 0 1 772755 0 0 0 0 0 1 775659 0 0 0 0 0
Could you maybe help me solve this issue? Cheers, Teodora