crash when plotting purity/ploidy

[apsteinberg]

Hi,

Thanks for building this exciting new tool! I am running into another issue which seems to stem from plotting purity/ploidy. Wakhan is crashing for some of my samples with this error message:

[2025-11-05 12:31:13] INFO: Generating BAFs for chr21
[2025-11-05 12:31:15] INFO: Generating BAFs for chr22
[2025-11-05 12:31:17] INFO: Generating BAFs for chrX
[2025-11-05 12:31:27] INFO: Generating BAFs for chrY
Traceback (most recent call last):
  File "/opt/wakhan/Wakhan/wakhan.py", line 28, in <module>
    main()
  File "/opt/wakhan/Wakhan/wakhan.py", line 24, in main
    sys.exit(main())
  File "/opt/wakhan/Wakhan/src/main.py", line 357, in main
    wakhan_all(args) #hapcorrect + cna
  File "/opt/wakhan/Wakhan/src/main.py", line 373, in wakhan_all
    cna_process(args) #cna
  File "/opt/wakhan/Wakhan/src/main.py", line 595, in cna_process
    copy_numbers_assignment_haplotypes(args, tumor_cov, max_limit, single_copy_cov, centers, subclonals, df_hp1, df_hp2, df_segs_hp1, df_segs_hp2, snps_cpd_means_df, csv_df_snps_mean, df_snps_in_csv, df_unphased, x_axis, observed_hist, False)
  File "/opt/wakhan/Wakhan/src/main.py", line 114, in copy_numbers_assignment_haplotypes
    plot_ploidy_purity_p_values(args, [data[n][0] for n in range(len(data))], [data[n][1] for n in range(len(data))], [data[n][3] for n in range(len(data))])
  File "/opt/wakhan/Wakhan/src/plots.py", line 5500, in plot_ploidy_purity_p_values
    if (purity_values[0] < float(args.purity_range.split('-')[0]) or purity_values[0] > float(args.purity_range.split('-')[1])) or (
IndexError: list index out of range

my run command is:

wakhan \
    --bin-size 50000 --contigs chr1-22,chrX,chrY --phaseblocks-enable --loh-enable --copynumbers-subclonal-enable \
    --use-sv-haplotypes \
    --user-input-genes /data1/shahs3/reference/ref-sarcoma/GRCh38/grch38_genes.tsv \
     \
    --threads 24 \
    --reference GRCh38.primary_assembly.genome.fa \
    --target-bam SHAH_H004080_T01_01_WG01.tumor.haplotagged.bam \
    --normal-phased-vcf SHAH_H004080_T01_01_WG01.vcf.gz \
    --genome-name SHAH_H004080_T01_01_WG01 \
    --breakpoints severus_somatic.vcf \
    --out-dir-plots .

Any clues to what is going on here?

Thanks for your time and help.

Best,
Asher

[tahashmi]

So you mean, your multiple samples are crashing here at the same point? Could you please put this function call under this condition and rerun cna() module and share the log here?

[apsteinberg]

Yes, multiple samples are crashing at this point. I can do that -- is there a flag for this? For some reason not seeing it.

Thanks,
Asher