tlesluyes
commented
7 months ago Hi @CHENAO-QIAN,
Is your BAM indexed? If yes, is the index located where the BAM is (same folder)? If yes, can you try re-indexing it?
This issue is related to alleleCounter. If the issue persists, try running alleleCounter manually with:
alleleCounter -l $myPath1/G1000_alleles_hg38_chr1.txt -b $myPath2/HR15AE5E5.trimmomatic1_tumor_markdup.bam -o out_chr1.txt. This will help us understand what is going on.
Cheers,
Tom.
CHENAO-QIAN
sunnaa0423
Hi I am trying to run ascat.prepareHTS function on the wes data:
ASCAT::ascat.prepareHTS(tumourseqfile =paste0(data_dir,"BAM/HR15AE5E5.trimmomatic1_tumor_markdup.bam"), normalseqfile =paste0(data_dir,"BAM/HR15AE5E5.trimmomatic1_normal_markdup.bam"), tumourname ="HR15AE5E5", normalname ="HR15AE1E1", allelecounter_exe = "/hpc/scratch/nvme4/cq038719/alleleCounter/bin/alleleCounter", alleles.prefix = paste0(output_dir,"/data/G1000_allelesAll_hg38/G1000_alleles_hg38_chr"), loci.prefix = paste0(output_dir,"/data/G1000_lociAll_hg38/G1000_loci_hg38_chr"), gender = "XX", genomeVersion = "hg38", nthreads = 15, tumourLogR_file = "Tumor_LogR.txt", tumourBAF_file = "Tumor_BAF.txt", normalLogR_file = "Germline_LogR.txt", normalBAF_file = "Germline_BAF.txt", BED_file = paste0(data_dir,"Twist_Comprehensive_Exome_Covered_Targets_hg38.bed") )
It's giving me an error: 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: Cannot allocate memory) 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. Error in `/hpc/scratch/nvme4/cq038719/alleleCounter/bin/alleleCounter': munmap_chunk(): invalid pointer: 0x00007fffffffe1ba
I tried to search for similar error but had no luck. Thank you in advance!