python wakhan.py \
  --reference          "${REF}" \
  --target-bam         "${TUMOUR_BAM}" \
  --genome-name        "${TUMOUR_NAME}" \
  --normal-phased-vcf  "${NORMAL_PHASED_SNV_VCF}" \
  --breakpoints        "${TUMOUR_SV_VCF}" \
  --out-dir-plots      "${OUTPUT_DIR}/${SAMPLE}_T" \
  --loh-enable \
  --cpd-internal-segments \
  --pdf-enable \
  --threads            10 \
  --without-phasing \
  --phaseblock-flipping-disable \
  --histogram-coverage

[2025-07-08 14:42:49] INFO: Starting Wakhan 0.1.1
[2025-07-08 14:42:49] INFO: Cmd: /nobackup/[...]/chrm_testing/Wakhan/wakhan.py --reference /mnt/storage/nobackup/proj/chlg/re_aligned_files/hg38.fa --target-bam /mnt/storage/nobackup/proj/chlg/re_aligned_files/[...].aligned.bam --genome-name  --normal-phased-vcf /nobackup/njb440/chrm_testing/clair3/[...]/phased_merge_output.vcf.gz --breakpoints /nobackup/njb440/chrm_testing/severus/[...]/somatic_SVs/severus_somatic.vcf --out-dir-plots /nobackup/njb440/chrm_testing/wakhan_nophase/[..] --loh-enable --cpd-internal-segments --pdf-enable --threads 10 --without-phasing --phaseblock-flipping-disable --histogram-coverage
[2025-07-08 14:42:49] INFO: Python version: 3.8.0 | packaged by conda-forge | (default, Nov 22 2019, 19:11:38) 
[GCC 7.3.0]
[2025-07-08 14:42:50] INFO: Parsing reads from ['/mnt/storage/nobackup/proj/chlg/re_aligned_files_[...]/[...].aligned.bam']
[2025-07-08 14:48:54] INFO: Parsed 1873495 segments
[2025-07-08 14:48:54] INFO: Computing coverage histogram
[2025-07-08 14:49:37] INFO: Split variants = True
[2025-07-08 14:49:37] INFO: check info = True
[2025-07-08 14:49:37] INFO: Allele symbol = 0
[2025-07-08 14:49:37] INFO: Initializing HeaderParser
[2025-07-08 14:49:37] INFO: Reading vcf form file /nobackup/njb440/chrm_testing/severus/[...]/somatic_SVs/severus_somatic.vcf
[2025-07-08 14:49:37] INFO: Setting self.individuals to ['[...].aligned']
[2025-07-08 14:49:38] INFO: Computing coverage for bins
[2025-07-08 14:49:42] INFO: Writing coverage for bins
[2025-07-08 14:49:42] INFO: Parsing phaseblocks information
[2025-07-08 14:49:42] INFO: bcftools -> Query for phasesets and GT, DP, VAF feilds by creating a CSV file
[2025-07-08 14:50:06] INFO: Computing coverage for phaseblocks
[2025-07-08 14:50:07] INFO: Writing coverage for phaseblocks
[2025-07-08 14:50:07] INFO: Loading coverage (bins) and coverage (phaseblocks) files...
[2025-07-08 14:50:07] INFO: Generating coverage plots chromosomes-wise
[2025-07-08 14:50:07] INFO: Split variants = True
[2025-07-08 14:50:07] INFO: check info = True
[2025-07-08 14:50:07] INFO: Allele symbol = 0
[2025-07-08 14:50:07] INFO: Initializing HeaderParser
[2025-07-08 14:50:07] INFO: Reading vcf form file /nobackup/njb440/chrm_testing/severus/[...]/somatic_SVs/severus_somatic.vcf
[2025-07-08 14:50:07] INFO: Setting self.individuals to ['[...].aligned']
[2025-07-08 14:50:07] INFO: Split variants = True
[2025-07-08 14:50:07] INFO: check info = True
[2025-07-08 14:50:07] INFO: Allele symbol = 0
[2025-07-08 14:50:07] INFO: Initializing HeaderParser
[2025-07-08 14:50:07] INFO: Reading vcf form file /nobackup/njb440/chrm_testing/severus/[...]/somatic_SVs/severus_somatic.vcf
[2025-07-08 14:50:07] INFO: Setting self.individuals to ['[...].aligned']
[2025-07-08 14:50:07] INFO: Plots generation for chr1
[2025-07-08 14:50:12] INFO: Plots generation for chr2
[2025-07-08 14:50:13] INFO: Plots generation for chr3
[2025-07-08 14:50:14] INFO: Plots generation for chr4
[2025-07-08 14:50:15] INFO: Plots generation for chr5
[2025-07-08 14:50:16] INFO: Plots generation for chr6
[2025-07-08 14:50:17] INFO: Plots generation for chr7
[2025-07-08 14:50:18] INFO: Plots generation for chr8
[2025-07-08 14:50:19] INFO: Plots generation for chr9
[2025-07-08 14:50:20] INFO: Plots generation for chr10
[2025-07-08 14:50:21] INFO: Plots generation for chr11
[2025-07-08 14:50:21] INFO: Plots generation for chr12
[2025-07-08 14:50:22] INFO: Plots generation for chr13
[2025-07-08 14:50:23] INFO: Plots generation for chr14
[2025-07-08 14:50:24] INFO: Plots generation for chr15
[2025-07-08 14:50:24] INFO: Plots generation for chr16
[2025-07-08 14:50:25] INFO: Plots generation for chr17
[2025-07-08 14:50:26] INFO: Plots generation for chr18
[2025-07-08 14:50:26] INFO: Plots generation for chr19
[2025-07-08 14:50:27] INFO: Plots generation for chr20
[2025-07-08 14:50:27] INFO: Plots generation for chr21
[2025-07-08 14:50:28] INFO: Plots generation for chr22
[2025-07-08 14:50:28] INFO: Plots generation for chrX
[2025-07-08 14:50:29] INFO: Generating optimal clusters plots for bins
[2025-07-08 14:50:29] INFO: Max limit for normal optimization: 22
[2025-07-08 14:50:29] INFO: Tumor coverage: 69.39656902523504
[2025-07-08 14:50:29] INFO: First minimum 8
[2025-07-08 14:50:29] INFO: Max correlation peak 25
[2025-07-08 14:50:29] INFO: Half peak: True
[2025-07-08 14:50:29] INFO: Estimated single copy coverage: 25.012
[2025-07-08 14:50:29] INFO: Initial detected clusters means: [0.0, 25.012, 50.024, 75.036]
[2025-07-08 14:50:29] INFO: Loading and sorting SNPs df
Traceback (most recent call last):
  File "/nobackup/njb440/chrm_testing/Wakhan/wakhan.py", line 28, in <module>
    main()
  File "/nobackup/njb440/chrm_testing/Wakhan/wakhan.py", line 24, in main
    sys.exit(main())
  File "/mnt/storage/nobackup/njb440/chrm_testing/Wakhan/src/main.py", line 499, in main
    df_snps_in_csv = snps_df_loh(args, thread_pool, df_hp1)
  File "/mnt/storage/nobackup/njb440/chrm_testing/Wakhan/src/snps_loh.py", line 69, in snps_df_loh
    df_snps_frequencies = csv_df_chromosomes_sorter(args.out_dir_plots+'/data/snps_frequencies.csv', ['chr', 'pos', 'freq_value_a', 'hp_a', 'freq_value_b', 'hp_b'])
  File "/mnt/storage/nobackup/njb440/chrm_testing/Wakhan/src/utils.py", line 454, in csv_df_chromosomes_sorter
    dataframe = pd.read_csv(path, sep=sept, names=names)
  File "/mnt/nfs/home/njb440/.conda/envs/wakhan-env/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
  File "/mnt/nfs/home/njb440/.conda/envs/wakhan-env/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/mnt/nfs/home/njb440/.conda/envs/wakhan-env/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
  File "/mnt/nfs/home/njb440/.conda/envs/wakhan-env/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
  File "/mnt/nfs/home/njb440/.conda/envs/wakhan-env/lib/python3.8/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
FileNotFoundError: [Errno 2] No such file or directory: '/nobackup/njb440/[...]/snps_frequencies.csv'