Running HATCHet with phasing

[um-pdavila]

Good evening,

Is Running HATCHet with phasing still currently a two part process as indicated in the hatchet README.html file?
http://compbio.cs.brown.edu/hatchet/script/README.html

We are stuck at the cluster_bins run, details below. Any guidance would be greatly appreciated.

We have run genotype_snps, phase_snps, download_panel, count_alleles, count_reads, and combine_counts independently, setting each, one at a time, to True, and the others to false. For example:

[run]
genotype_snps=False
phase_snps=False
download_panel=False
count_alleles = False
count_reads = False
combine_counts = False
cluster_bins = True
plot_bins = False
compute_cn = False
plot_cn = False

(hatchet_1.1.1) [username@node HATCHet]$ hatchet run hatchet.7-7-23.ini
[2023-Jul-07 02:57:40]# Parsing and checking input arguments
 
        bbfile: PATH_TO/HATCHet/output_7-7-23/bb/bulk.bb
        diploidbaf: 0.1
        seed: 0
        decoding: map
        minK: 2
        maxK: 30
        exactK: 0
        covar: diag
        transmat: diag
        tau: 1e-06
        outsegments: PATH_TO/HATCHet/output_7-7-23/bbc/bulk.seg
        outbins: PATH_TO/HATCHet/output_7-7-23/bbc/bulk.bbc
[2023-Jul-07 02:57:40]# Reading the combined BB file
[2023-Jul-07 02:57:42]# Clustering bins by RD and BAF across tumor samples using locality
Model is not converging.  Current: 39973.612034460035 is not greater than 39973.64436343625. Delta is -0.03232897621637676
Model is not converging.  Current: 41561.64143230467 is not greater than 41561.66624473987. Delta is -0.024812435200146865
Model is not converging.  Current: 43591.67327317303 is not greater than 43591.74561723709. Delta is -0.07234406405768823
Model is not converging.  Current: 44043.04258445045 is not greater than 44043.104144543446. Delta is -0.06156009299593279
Model is not converging.  Current: 45219.111067996564 is not greater than 45219.16396330124. Delta is -0.052895304674166255
Model is not converging.  Current: 46000.33344260872 is not greater than 46000.37931941253. Delta is -0.045876803815190215
/sccc/share/apps/miniconda3/envs/hatchet_1.1.1/lib/python3.9/site-packages/hmmlearn/hmm.py:340: RuntimeWarning: invalid value encountered in divide
  self.means_ = ((means_weight * means_prior + stats['obs'])
Traceback (most recent call last):
  File "/sccc/share/apps/miniconda3/envs/hatchet_1.1.1/bin/hatchet", line 33, in 
    sys.exit(load_entry_point('hatchet==1.1.1', 'console_scripts', 'hatchet')())
  File "/sccc/share/apps/miniconda3/envs/hatchet_1.1.1/lib/python3.9/site-packages/hatchet/__main__.py", line 61, in main
    globals()[command](args)
  File "/sccc/share/apps/miniconda3/envs/hatchet_1.1.1/lib/python3.9/site-packages/hatchet/utils/run.py", line 316, in main
    cluster_bins(
  File "/sccc/share/apps/miniconda3/envs/hatchet_1.1.1/lib/python3.9/site-packages/hatchet/utils/cluster_bins.py", line 47, in main
    (best_score, best_model, best_labels, best_K, results,) = hmm_model_select(
  File "/sccc/share/apps/miniconda3/envs/hatchet_1.1.1/lib/python3.9/site-packages/hatchet/utils/cluster_bins.py", line 258, in hmm_model_select
    prob, labels = model.decode(X, lengths, algorithm=decode_alg)
  File "/sccc/share/apps/miniconda3/envs/hatchet_1.1.1/lib/python3.9/site-packages/hmmlearn/base.py", line 324, in decode
    self._check()
  File "/sccc/share/apps/miniconda3/envs/hatchet_1.1.1/lib/python3.9/site-packages/hmmlearn/hmm.py", line 313, in _check
    super()._check()
  File "/sccc/share/apps/miniconda3/envs/hatchet_1.1.1/lib/python3.9/site-packages/hmmlearn/base.py", line 949, in _check
    self._check_sum_1("startprob_")
  File "/sccc/share/apps/miniconda3/envs/hatchet_1.1.1/lib/python3.9/site-packages/hmmlearn/base.py", line 931, in _check_sum_1
    raise ValueError(
ValueError: startprob_ must sum to 1 (got nan)

Thank you for your time.

Best,
Pedro