Failed at step of Computing coverage histogram

[thangnx1012]

Hi again,

I have several ONT tumor-only BAM files, which were aligned with the same workflow for both hg38 and CHM13 reference genomes. Most of them work well with WAKHAN 0.1.0, but only two from hg38-references showed the problem like this:

WAKHAN indentify CNA for abc_nanopore_hg38_sorted.bam
[2025-03-04 09:33:43] INFO: Starting Wakhan 0.1.0
[2025-03-04 09:33:43] INFO: Cmd: software/Wakhan/wakhan.py --threads 50 --reference references/Homo_sapiens_assembly38_masked_noALT.fa --target-bam longphase_SNP_SV/abc_nanopore_hg38_haplotagged.bam --tumor-vcf longphase_SNP_SV/abc_nanopore_hg38_SV_SNP.vcf.gz --genome-name abc_nanopore_hg38 --reference-name hg38 --contigs chr1-22,X,Y --pdf-enable --out-dir-plots abc_nanopore_hg38 --breakpoints abc_nanopore_hg38/all_SVs/severus_all.vcf
[2025-03-04 09:33:43] INFO: Python version: 3.8.0 | packaged by conda-forge | (default, Nov 22 2019, 19:11:38)
[GCC 7.3.0]
[2025-03-04 09:33:49] INFO: Split variants = True
[2025-03-04 09:33:49] INFO: check info = True
[2025-03-04 09:33:49] INFO: Allele symbol = 0
[2025-03-04 09:33:49] INFO: Initializing HeaderParser
[2025-03-04 09:33:49] INFO: Reading vcf form file severus/abc_nanopore_hg38/all_SVs/severus_all.vcf
[2025-03-04 09:33:49] INFO: Setting self.individuals to ['abc_nanopore_hg38_haplotagged']
[2025-03-04 09:33:52] INFO: Parsing reads from longphase/longphase_SNP_SV/abc_nanopore_hg38_haplotagged.bam
[2025-03-04 10:28:37] INFO: Parsed 22840902 segments
[2025-03-04 10:28:38] INFO: Computing coverage histogram
Traceback (most recent call last):
File "/staging/leuven/stg_00096/home/thangnx/software/Wakhan/wakhan.py", line 28, in
main()
File "/staging/leuven/stg_00096/home/thangnx/software/Wakhan/wakhan.py", line 24, in main
sys.exit(main())
File "/lustre1/project/stg_00096/home/thangnx/software/Wakhan/src/main.py", line 272, in main
main_process(args, breakpoints_additional) #hapcorrect
File "/lustre1/project/stg_00096/home/thangnx/software/Wakhan/src/hapcorrect/src/main_hapcorrect.py", line 78, in main_process
coverage_histograms = update_coverage_hist(genome_ids, ref_lengths, segments_by_read, args.min_mapping_quality,
File "/lustre1/project/stg_00096/home/thangnx/software/Wakhan/src/hapcorrect/src/process_bam.py", line 257, in update_coverage_hist
coverage_histograms[(read.genome_id, read.haplotype, read.ref_id)][i] += 1
IndexError: list index out of range

Here is my slurm_jobs
samtool index ${longphase_outdir}/${samplename}_haplotagged.bam
python ${wakhan}/wakhan.py --threads 50
--reference ${hg38_reference}
--target-bam ${longphase_outdir}/${samplename}_haplotagged.bam
--tumor-vcf ${longphase_outdir}/${samplename}_SV_SNP.vcf.gz
--genome-name ${samplename}
--reference-name hg38
--contigs chr1-22,X,Y
--pdf-enable
--out-dir-plots $wakhan_outdir/${samplename}
--breakpoints ${severus_outdir}/${samplename}/all_SVs/severus_all.vcf