Inference from a test VCF file#
Try to infer a tstree object like I did with nf-treeseq pipeline but using the
sample VCF provided in sheepTSexample
import cyvcf2
import tsinfer
import tsdate
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
from tskitetude import get_project_dir
from tskitetude.helper import get_chromosome_lengths, add_diploid_sites, create_windows
Configure tskitetude module to use tqdm.notebook:
from tqdm.notebook import tqdm
import tskitetude.helper
tskitetude.helper.tqdm = tqdm
vcf_file = str(get_project_dir() / "experiments/test1M/test1M.out.inf.vcf.gz")
vcf = cyvcf2.VCF(vcf_file)
chromosome_lengths = get_chromosome_lengths(vcf)
# get first variant like I did in the helper script
variant = next(vcf)
sequence_length = chromosome_lengths[variant.CHROM]
print(f"Getting information for chromosome {variant.CHROM} with length {sequence_length} bp")
Getting information for chromosome 1 with length 1000000 bp
Create SampleData object. Add additional information (as we did in tutorial):
# reset the VCF file
vcf = cyvcf2.VCF(vcf_file)
with tsinfer.SampleData(
path = str(get_project_dir() / "experiments/test1M/test1M.out.inf.samples"),
sequence_length = sequence_length) as samples:
# add population information (optional)
samples.add_population(metadata={"name": "Mouflon"})
samples.add_population(metadata={"name": "Iranian"})
samples.add_population(metadata={"name": "Border"})
# add individuals (optional)
# create a population lookup list to iterate over
popID = np.repeat([0,1,2], [5, 50, 50]).tolist()
# track added individuals
indv_lookup = {}
for i in range(105):
indv_lookup[f"tsk_{i}"] = samples.add_individual(ploidy=2, population=popID[i], metadata={"name": f"tsk_{i}"})
add_diploid_sites(
vcf,
samples,
ancestors_alleles={},
indv_lookup=indv_lookup,
allele_chars=set("01"),
ancestral_method="reference"
)
print(
f"Sample file created for {samples.num_samples} samples "
f"({samples.num_individuals} individuals) "
f"with {samples.num_sites} variable sites."
)
/home/cozzip/.cache/pypoetry/virtualenvs/tskitetude-hh-GIRXc-py3.12/lib/python3.12/site-packages/tsinfer/formats.py:530: FutureWarning: The LMDBStore is deprecated and will be removed in a Zarr-Python version 3, see https://github.com/zarr-developers/zarr-python/issues/1274 for more information.
return zarr.LMDBStore(self.path, subdir=False, map_size=map_size)
/tmp/ipykernel_44164/3058575067.py:4: DeprecationWarning: SampleData is deprecated
with tsinfer.SampleData(
2025-12-19 13:28:16,852 - tskitetude.helper - INFO - Using reference allele as ancestral allele
Duplicate entries at position 83850, ignoring all but the first
Duplicate entries at position 119222, ignoring all but the first
Duplicate entries at position 176965, ignoring all but the first
Duplicate entries at position 214451, ignoring all but the first
Duplicate entries at position 231728, ignoring all but the first
Duplicate entries at position 232122, ignoring all but the first
Duplicate entries at position 233613, ignoring all but the first
Duplicate entries at position 250950, ignoring all but the first
Duplicate entries at position 289598, ignoring all but the first
Duplicate entries at position 355578, ignoring all but the first
Duplicate entries at position 368226, ignoring all but the first
Duplicate entries at position 380744, ignoring all but the first
Duplicate entries at position 389742, ignoring all but the first
Duplicate entries at position 401443, ignoring all but the first
Duplicate entries at position 423892, ignoring all but the first
Duplicate entries at position 463723, ignoring all but the first
Duplicate entries at position 484903, ignoring all but the first
Duplicate entries at position 497351, ignoring all but the first
Duplicate entries at position 530338, ignoring all but the first
Duplicate entries at position 533058, ignoring all but the first
Duplicate entries at position 547183, ignoring all but the first
Duplicate entries at position 559588, ignoring all but the first
Duplicate entries at position 585695, ignoring all but the first
Duplicate entries at position 588075, ignoring all but the first
Duplicate entries at position 641377, ignoring all but the first
Duplicate entries at position 668752, ignoring all but the first
Duplicate entries at position 685839, ignoring all but the first
Duplicate entries at position 708451, ignoring all but the first
Duplicate entries at position 708624, ignoring all but the first
Duplicate entries at position 738714, ignoring all but the first
Duplicate entries at position 771513, ignoring all but the first
Duplicate entries at position 796270, ignoring all but the first
Duplicate entries at position 801989, ignoring all but the first
Duplicate entries at position 842642, ignoring all but the first
Duplicate entries at position 844811, ignoring all but the first
Duplicate entries at position 849212, ignoring all but the first
Duplicate entries at position 869978, ignoring all but the first
Duplicate entries at position 901725, ignoring all but the first
Duplicate entries at position 917886, ignoring all but the first
Duplicate entries at position 925039, ignoring all but the first
Duplicate entries at position 950803, ignoring all but the first
Sample file created for 210 samples (105 individuals) with 12844 variable sites.
/home/cozzip/.cache/pypoetry/virtualenvs/tskitetude-hh-GIRXc-py3.12/lib/python3.12/site-packages/tsinfer/formats.py:104: FutureWarning: The LMDBStore is deprecated and will be removed in a Zarr-Python version 3, see https://github.com/zarr-developers/zarr-python/issues/1274 for more information.
store = zarr.LMDBStore(
# Do the inference
sparrow_ts = tsinfer.infer(
samples,
num_threads=4
)
# Simplify the tree sequence
ts = sparrow_ts.simplify()
print(
f"Inferred tree sequence `ts`: {ts.num_trees} "
f"trees over {ts.sequence_length / 1e6} Mb"
)
2025-12-19 13:28:21,272 - root - INFO - Max encoded genotype matrix size=2.6 MiB
2025-12-19 13:28:21,273 - tsinfer.inference - INFO - Starting addition of 12844 sites
2025-12-19 13:28:21,616 - tsinfer.inference - INFO - Finished adding sites
2025-12-19 13:28:21,622 - tsinfer.inference - INFO - Ancestor builder peak RAM: 2.0 MiB
2025-12-19 13:28:21,658 - tsinfer.inference - INFO - Starting build for 6469 ancestors
2025-12-19 13:28:23,695 - tsinfer.inference - INFO - Finished building ancestors
2025-12-19 13:28:23,770 - tsinfer.inference - INFO - Mismatch prevented by setting constant high recombination and low mismatch probabilities
2025-12-19 13:28:23,771 - tsinfer.inference - INFO - Summary of recombination probabilities between sites: min=0.01; max=0.01; median=0.01; mean=0.01
2025-12-19 13:28:23,772 - tsinfer.inference - INFO - Summary of mismatch probabilities over sites: min=1e-20; max=1e-20; median=1e-20; mean=1e-20
2025-12-19 13:28:23,773 - tsinfer.inference - INFO - Matching using likelihood_threshold of 1e-13
2025-12-19 13:28:23,779 - tsinfer.inference - INFO - 207 epochs with 13.0 median size.
2025-12-19 13:28:23,779 - tsinfer.inference - INFO - First large (>6500.0) epoch is 207
2025-12-19 13:28:23,780 - tsinfer.inference - INFO - Grouping 6471 ancestors by linesweep
2025-12-19 13:28:23,788 - tsinfer.ancestors - INFO - Merged to 897 ancestors in 0.01s
2025-12-19 13:28:23,788 - tsinfer.ancestors - INFO - Built 1794 events in 0.00s
2025-12-19 13:28:24,430 - tsinfer.ancestors - INFO - Linesweep generated 125220 dependencies in 0.64s
2025-12-19 13:28:25,005 - tsinfer.ancestors - INFO - Found groups in 0.57s
2025-12-19 13:28:25,009 - tsinfer.ancestors - INFO - Un-merged in 0.00s
2025-12-19 13:28:25,010 - tsinfer.ancestors - INFO - 194 groups with median size 13.0
2025-12-19 13:28:25,012 - tsinfer.inference - INFO - Finished grouping into 194 groups in 1.23 seconds
2025-12-19 13:28:25,013 - tsinfer.inference - INFO - Starting ancestor matching for 194 groups
2025-12-19 13:28:25,014 - tsinfer.inference - INFO - Starting group 0 of 194 with 0 ancestors
2025-12-19 13:28:25,024 - tsinfer.inference - INFO - Finished group 0 of 194 in 0.01 seconds
2025-12-19 13:28:25,025 - tsinfer.inference - INFO - Starting group 1 of 194 with 1 ancestors
2025-12-19 13:28:25,051 - tsinfer.inference - INFO - Finished group 1 of 194 in 0.03 seconds
2025-12-19 13:28:25,052 - tsinfer.inference - INFO - Starting group 2 of 194 with 25 ancestors
2025-12-19 13:28:25,073 - tsinfer.inference - INFO - Finished group 2 of 194 in 0.02 seconds
2025-12-19 13:28:25,074 - tsinfer.inference - INFO - Starting group 3 of 194 with 19 ancestors
2025-12-19 13:28:25,092 - tsinfer.inference - INFO - Finished group 3 of 194 in 0.02 seconds
2025-12-19 13:28:25,093 - tsinfer.inference - INFO - Starting group 4 of 194 with 25 ancestors
2025-12-19 13:28:25,113 - tsinfer.inference - INFO - Finished group 4 of 194 in 0.02 seconds
2025-12-19 13:28:25,114 - tsinfer.inference - INFO - Starting group 5 of 194 with 18 ancestors
2025-12-19 13:28:25,133 - tsinfer.inference - INFO - Finished group 5 of 194 in 0.02 seconds
2025-12-19 13:28:25,134 - tsinfer.inference - INFO - Starting group 6 of 194 with 13 ancestors
2025-12-19 13:28:25,155 - tsinfer.inference - INFO - Finished group 6 of 194 in 0.02 seconds
2025-12-19 13:28:25,157 - tsinfer.inference - INFO - Starting group 7 of 194 with 11 ancestors
2025-12-19 13:28:25,174 - tsinfer.inference - INFO - Finished group 7 of 194 in 0.02 seconds
2025-12-19 13:28:25,175 - tsinfer.inference - INFO - Starting group 8 of 194 with 8 ancestors
2025-12-19 13:28:25,192 - tsinfer.inference - INFO - Finished group 8 of 194 in 0.02 seconds
2025-12-19 13:28:25,192 - tsinfer.inference - INFO - Starting group 9 of 194 with 4 ancestors
2025-12-19 13:28:25,207 - tsinfer.inference - INFO - Finished group 9 of 194 in 0.01 seconds
2025-12-19 13:28:25,208 - tsinfer.inference - INFO - Starting group 10 of 194 with 1 ancestors
2025-12-19 13:28:25,222 - tsinfer.inference - INFO - Finished group 10 of 194 in 0.01 seconds
2025-12-19 13:28:25,223 - tsinfer.inference - INFO - Starting group 11 of 194 with 12 ancestors
2025-12-19 13:28:25,248 - tsinfer.inference - INFO - Finished group 11 of 194 in 0.03 seconds
2025-12-19 13:28:25,250 - tsinfer.inference - INFO - Starting group 12 of 194 with 13 ancestors
2025-12-19 13:28:25,274 - tsinfer.inference - INFO - Finished group 12 of 194 in 0.02 seconds
2025-12-19 13:28:25,276 - tsinfer.inference - INFO - Starting group 13 of 194 with 12 ancestors
2025-12-19 13:28:25,298 - tsinfer.inference - INFO - Finished group 13 of 194 in 0.02 seconds
2025-12-19 13:28:25,300 - tsinfer.inference - INFO - Starting group 14 of 194 with 11 ancestors
2025-12-19 13:28:25,324 - tsinfer.inference - INFO - Finished group 14 of 194 in 0.02 seconds
2025-12-19 13:28:25,326 - tsinfer.inference - INFO - Starting group 15 of 194 with 17 ancestors
2025-12-19 13:28:25,352 - tsinfer.inference - INFO - Finished group 15 of 194 in 0.03 seconds
2025-12-19 13:28:25,353 - tsinfer.inference - INFO - Starting group 16 of 194 with 11 ancestors
2025-12-19 13:28:25,373 - tsinfer.inference - INFO - Finished group 16 of 194 in 0.02 seconds
2025-12-19 13:28:25,375 - tsinfer.inference - INFO - Starting group 17 of 194 with 13 ancestors
2025-12-19 13:28:25,397 - tsinfer.inference - INFO - Finished group 17 of 194 in 0.02 seconds
2025-12-19 13:28:25,399 - tsinfer.inference - INFO - Starting group 18 of 194 with 10 ancestors
2025-12-19 13:28:25,419 - tsinfer.inference - INFO - Finished group 18 of 194 in 0.02 seconds
2025-12-19 13:28:25,421 - tsinfer.inference - INFO - Starting group 19 of 194 with 13 ancestors
2025-12-19 13:28:25,444 - tsinfer.inference - INFO - Finished group 19 of 194 in 0.02 seconds
2025-12-19 13:28:25,445 - tsinfer.inference - INFO - Starting group 20 of 194 with 10 ancestors
2025-12-19 13:28:25,469 - tsinfer.inference - INFO - Finished group 20 of 194 in 0.02 seconds
2025-12-19 13:28:25,470 - tsinfer.inference - INFO - Starting group 21 of 194 with 14 ancestors
2025-12-19 13:28:25,498 - tsinfer.inference - INFO - Finished group 21 of 194 in 0.03 seconds
2025-12-19 13:28:25,498 - tsinfer.inference - INFO - Starting group 22 of 194 with 17 ancestors
2025-12-19 13:28:25,530 - tsinfer.inference - INFO - Finished group 22 of 194 in 0.03 seconds
2025-12-19 13:28:25,531 - tsinfer.inference - INFO - Starting group 23 of 194 with 13 ancestors
2025-12-19 13:28:25,557 - tsinfer.inference - INFO - Finished group 23 of 194 in 0.03 seconds
2025-12-19 13:28:25,559 - tsinfer.inference - INFO - Starting group 24 of 194 with 10 ancestors
2025-12-19 13:28:25,582 - tsinfer.inference - INFO - Finished group 24 of 194 in 0.02 seconds
2025-12-19 13:28:25,583 - tsinfer.inference - INFO - Starting group 25 of 194 with 8 ancestors
2025-12-19 13:28:25,607 - tsinfer.inference - INFO - Finished group 25 of 194 in 0.02 seconds
2025-12-19 13:28:25,608 - tsinfer.inference - INFO - Starting group 26 of 194 with 13 ancestors
2025-12-19 13:28:25,636 - tsinfer.inference - INFO - Finished group 26 of 194 in 0.03 seconds
2025-12-19 13:28:25,638 - tsinfer.inference - INFO - Starting group 27 of 194 with 9 ancestors
2025-12-19 13:28:25,663 - tsinfer.inference - INFO - Finished group 27 of 194 in 0.02 seconds
2025-12-19 13:28:25,664 - tsinfer.inference - INFO - Starting group 28 of 194 with 8 ancestors
2025-12-19 13:28:25,687 - tsinfer.inference - INFO - Finished group 28 of 194 in 0.02 seconds
2025-12-19 13:28:25,688 - tsinfer.inference - INFO - Starting group 29 of 194 with 9 ancestors
2025-12-19 13:28:25,714 - tsinfer.inference - INFO - Finished group 29 of 194 in 0.03 seconds
2025-12-19 13:28:25,716 - tsinfer.inference - INFO - Starting group 30 of 194 with 8 ancestors
2025-12-19 13:28:25,740 - tsinfer.inference - INFO - Finished group 30 of 194 in 0.02 seconds
2025-12-19 13:28:25,742 - tsinfer.inference - INFO - Starting group 31 of 194 with 7 ancestors
2025-12-19 13:28:25,766 - tsinfer.inference - INFO - Finished group 31 of 194 in 0.02 seconds
2025-12-19 13:28:25,767 - tsinfer.inference - INFO - Starting group 32 of 194 with 9 ancestors
2025-12-19 13:28:25,795 - tsinfer.inference - INFO - Finished group 32 of 194 in 0.03 seconds
2025-12-19 13:28:25,796 - tsinfer.inference - INFO - Starting group 33 of 194 with 15 ancestors
2025-12-19 13:28:25,829 - tsinfer.inference - INFO - Finished group 33 of 194 in 0.03 seconds
2025-12-19 13:28:25,830 - tsinfer.inference - INFO - Starting group 34 of 194 with 12 ancestors
2025-12-19 13:28:25,862 - tsinfer.inference - INFO - Finished group 34 of 194 in 0.03 seconds
2025-12-19 13:28:25,863 - tsinfer.inference - INFO - Starting group 35 of 194 with 18 ancestors
2025-12-19 13:28:25,904 - tsinfer.inference - INFO - Finished group 35 of 194 in 0.04 seconds
2025-12-19 13:28:25,905 - tsinfer.inference - INFO - Starting group 36 of 194 with 15 ancestors
2025-12-19 13:28:25,947 - tsinfer.inference - INFO - Finished group 36 of 194 in 0.04 seconds
2025-12-19 13:28:25,948 - tsinfer.inference - INFO - Starting group 37 of 194 with 13 ancestors
2025-12-19 13:28:25,983 - tsinfer.inference - INFO - Finished group 37 of 194 in 0.03 seconds
2025-12-19 13:28:25,984 - tsinfer.inference - INFO - Starting group 38 of 194 with 11 ancestors
2025-12-19 13:28:26,015 - tsinfer.inference - INFO - Finished group 38 of 194 in 0.03 seconds
2025-12-19 13:28:26,017 - tsinfer.inference - INFO - Starting group 39 of 194 with 13 ancestors
2025-12-19 13:28:26,052 - tsinfer.inference - INFO - Finished group 39 of 194 in 0.04 seconds
2025-12-19 13:28:26,054 - tsinfer.inference - INFO - Starting group 40 of 194 with 10 ancestors
2025-12-19 13:28:26,086 - tsinfer.inference - INFO - Finished group 40 of 194 in 0.03 seconds
2025-12-19 13:28:26,086 - tsinfer.inference - INFO - Starting group 41 of 194 with 18 ancestors
2025-12-19 13:28:26,133 - tsinfer.inference - INFO - Finished group 41 of 194 in 0.05 seconds
2025-12-19 13:28:26,134 - tsinfer.inference - INFO - Starting group 42 of 194 with 13 ancestors
2025-12-19 13:28:26,175 - tsinfer.inference - INFO - Finished group 42 of 194 in 0.04 seconds
2025-12-19 13:28:26,176 - tsinfer.inference - INFO - Starting group 43 of 194 with 12 ancestors
2025-12-19 13:28:26,218 - tsinfer.inference - INFO - Finished group 43 of 194 in 0.04 seconds
2025-12-19 13:28:26,220 - tsinfer.inference - INFO - Starting group 44 of 194 with 13 ancestors
2025-12-19 13:28:26,262 - tsinfer.inference - INFO - Finished group 44 of 194 in 0.04 seconds
2025-12-19 13:28:26,263 - tsinfer.inference - INFO - Starting group 45 of 194 with 14 ancestors
2025-12-19 13:28:26,305 - tsinfer.inference - INFO - Finished group 45 of 194 in 0.04 seconds
2025-12-19 13:28:26,307 - tsinfer.inference - INFO - Starting group 46 of 194 with 8 ancestors
2025-12-19 13:28:26,337 - tsinfer.inference - INFO - Finished group 46 of 194 in 0.03 seconds
2025-12-19 13:28:26,339 - tsinfer.inference - INFO - Starting group 47 of 194 with 13 ancestors
2025-12-19 13:28:26,382 - tsinfer.inference - INFO - Finished group 47 of 194 in 0.04 seconds
2025-12-19 13:28:26,384 - tsinfer.inference - INFO - Starting group 48 of 194 with 5 ancestors
2025-12-19 13:28:26,415 - tsinfer.inference - INFO - Finished group 48 of 194 in 0.03 seconds
2025-12-19 13:28:26,416 - tsinfer.inference - INFO - Starting group 49 of 194 with 14 ancestors
2025-12-19 13:28:26,465 - tsinfer.inference - INFO - Finished group 49 of 194 in 0.05 seconds
2025-12-19 13:28:26,467 - tsinfer.inference - INFO - Starting group 50 of 194 with 17 ancestors
2025-12-19 13:28:26,524 - tsinfer.inference - INFO - Finished group 50 of 194 in 0.06 seconds
2025-12-19 13:28:26,526 - tsinfer.inference - INFO - Starting group 51 of 194 with 14 ancestors
2025-12-19 13:28:26,575 - tsinfer.inference - INFO - Finished group 51 of 194 in 0.05 seconds
2025-12-19 13:28:26,576 - tsinfer.inference - INFO - Starting group 52 of 194 with 9 ancestors
2025-12-19 13:28:26,615 - tsinfer.inference - INFO - Finished group 52 of 194 in 0.04 seconds
2025-12-19 13:28:26,617 - tsinfer.inference - INFO - Starting group 53 of 194 with 11 ancestors
2025-12-19 13:28:26,661 - tsinfer.inference - INFO - Finished group 53 of 194 in 0.04 seconds
2025-12-19 13:28:26,662 - tsinfer.inference - INFO - Starting group 54 of 194 with 18 ancestors
2025-12-19 13:28:26,721 - tsinfer.inference - INFO - Finished group 54 of 194 in 0.06 seconds
2025-12-19 13:28:26,722 - tsinfer.inference - INFO - Starting group 55 of 194 with 17 ancestors
2025-12-19 13:28:26,781 - tsinfer.inference - INFO - Finished group 55 of 194 in 0.06 seconds
2025-12-19 13:28:26,782 - tsinfer.inference - INFO - Starting group 56 of 194 with 9 ancestors
2025-12-19 13:28:26,823 - tsinfer.inference - INFO - Finished group 56 of 194 in 0.04 seconds
2025-12-19 13:28:26,824 - tsinfer.inference - INFO - Starting group 57 of 194 with 14 ancestors
2025-12-19 13:28:26,875 - tsinfer.inference - INFO - Finished group 57 of 194 in 0.05 seconds
2025-12-19 13:28:26,876 - tsinfer.inference - INFO - Starting group 58 of 194 with 7 ancestors
2025-12-19 13:28:26,910 - tsinfer.inference - INFO - Finished group 58 of 194 in 0.03 seconds
2025-12-19 13:28:26,911 - tsinfer.inference - INFO - Starting group 59 of 194 with 7 ancestors
2025-12-19 13:28:26,947 - tsinfer.inference - INFO - Finished group 59 of 194 in 0.04 seconds
2025-12-19 13:28:26,949 - tsinfer.inference - INFO - Starting group 60 of 194 with 13 ancestors
2025-12-19 13:28:27,006 - tsinfer.inference - INFO - Finished group 60 of 194 in 0.06 seconds
2025-12-19 13:28:27,007 - tsinfer.inference - INFO - Starting group 61 of 194 with 9 ancestors
2025-12-19 13:28:27,054 - tsinfer.inference - INFO - Finished group 61 of 194 in 0.05 seconds
2025-12-19 13:28:27,056 - tsinfer.inference - INFO - Starting group 62 of 194 with 13 ancestors
2025-12-19 13:28:27,114 - tsinfer.inference - INFO - Finished group 62 of 194 in 0.06 seconds
2025-12-19 13:28:27,115 - tsinfer.inference - INFO - Starting group 63 of 194 with 12 ancestors
2025-12-19 13:28:27,165 - tsinfer.inference - INFO - Finished group 63 of 194 in 0.05 seconds
2025-12-19 13:28:27,167 - tsinfer.inference - INFO - Starting group 64 of 194 with 11 ancestors
2025-12-19 13:28:27,217 - tsinfer.inference - INFO - Finished group 64 of 194 in 0.05 seconds
2025-12-19 13:28:27,219 - tsinfer.inference - INFO - Starting group 65 of 194 with 7 ancestors
2025-12-19 13:28:27,257 - tsinfer.inference - INFO - Finished group 65 of 194 in 0.04 seconds
2025-12-19 13:28:27,259 - tsinfer.inference - INFO - Starting group 66 of 194 with 12 ancestors
2025-12-19 13:28:27,312 - tsinfer.inference - INFO - Finished group 66 of 194 in 0.05 seconds
2025-12-19 13:28:27,314 - tsinfer.inference - INFO - Starting group 67 of 194 with 15 ancestors
2025-12-19 13:28:27,378 - tsinfer.inference - INFO - Finished group 67 of 194 in 0.06 seconds
2025-12-19 13:28:27,380 - tsinfer.inference - INFO - Starting group 68 of 194 with 14 ancestors
2025-12-19 13:28:27,444 - tsinfer.inference - INFO - Finished group 68 of 194 in 0.06 seconds
2025-12-19 13:28:27,445 - tsinfer.inference - INFO - Starting group 69 of 194 with 17 ancestors
2025-12-19 13:28:27,522 - tsinfer.inference - INFO - Finished group 69 of 194 in 0.08 seconds
2025-12-19 13:28:27,524 - tsinfer.inference - INFO - Starting group 70 of 194 with 12 ancestors
2025-12-19 13:28:27,580 - tsinfer.inference - INFO - Finished group 70 of 194 in 0.06 seconds
2025-12-19 13:28:27,580 - tsinfer.inference - INFO - Starting group 71 of 194 with 4 ancestors
2025-12-19 13:28:27,610 - tsinfer.inference - INFO - Finished group 71 of 194 in 0.03 seconds
2025-12-19 13:28:27,612 - tsinfer.inference - INFO - Starting group 72 of 194 with 14 ancestors
2025-12-19 13:28:27,675 - tsinfer.inference - INFO - Finished group 72 of 194 in 0.06 seconds
2025-12-19 13:28:27,676 - tsinfer.inference - INFO - Starting group 73 of 194 with 6 ancestors
2025-12-19 13:28:27,715 - tsinfer.inference - INFO - Finished group 73 of 194 in 0.04 seconds
2025-12-19 13:28:27,716 - tsinfer.inference - INFO - Starting group 74 of 194 with 14 ancestors
2025-12-19 13:28:27,781 - tsinfer.inference - INFO - Finished group 74 of 194 in 0.07 seconds
2025-12-19 13:28:27,782 - tsinfer.inference - INFO - Starting group 75 of 194 with 16 ancestors
2025-12-19 13:28:27,849 - tsinfer.inference - INFO - Finished group 75 of 194 in 0.07 seconds
2025-12-19 13:28:27,851 - tsinfer.inference - INFO - Starting group 76 of 194 with 10 ancestors
2025-12-19 13:28:27,904 - tsinfer.inference - INFO - Finished group 76 of 194 in 0.05 seconds
2025-12-19 13:28:27,906 - tsinfer.inference - INFO - Starting group 77 of 194 with 18 ancestors
2025-12-19 13:28:27,986 - tsinfer.inference - INFO - Finished group 77 of 194 in 0.08 seconds
2025-12-19 13:28:27,987 - tsinfer.inference - INFO - Starting group 78 of 194 with 13 ancestors
2025-12-19 13:28:28,054 - tsinfer.inference - INFO - Finished group 78 of 194 in 0.07 seconds
2025-12-19 13:28:28,056 - tsinfer.inference - INFO - Starting group 79 of 194 with 8 ancestors
2025-12-19 13:28:28,099 - tsinfer.inference - INFO - Finished group 79 of 194 in 0.04 seconds
2025-12-19 13:28:28,100 - tsinfer.inference - INFO - Starting group 80 of 194 with 13 ancestors
2025-12-19 13:28:28,170 - tsinfer.inference - INFO - Finished group 80 of 194 in 0.07 seconds
2025-12-19 13:28:28,171 - tsinfer.inference - INFO - Starting group 81 of 194 with 13 ancestors
2025-12-19 13:28:28,242 - tsinfer.inference - INFO - Finished group 81 of 194 in 0.07 seconds
2025-12-19 13:28:28,243 - tsinfer.inference - INFO - Starting group 82 of 194 with 10 ancestors
2025-12-19 13:28:28,303 - tsinfer.inference - INFO - Finished group 82 of 194 in 0.06 seconds
2025-12-19 13:28:28,304 - tsinfer.inference - INFO - Starting group 83 of 194 with 10 ancestors
2025-12-19 13:28:28,362 - tsinfer.inference - INFO - Finished group 83 of 194 in 0.06 seconds
2025-12-19 13:28:28,364 - tsinfer.inference - INFO - Starting group 84 of 194 with 9 ancestors
2025-12-19 13:28:28,421 - tsinfer.inference - INFO - Finished group 84 of 194 in 0.06 seconds
2025-12-19 13:28:28,422 - tsinfer.inference - INFO - Starting group 85 of 194 with 11 ancestors
2025-12-19 13:28:28,486 - tsinfer.inference - INFO - Finished group 85 of 194 in 0.06 seconds
2025-12-19 13:28:28,488 - tsinfer.inference - INFO - Starting group 86 of 194 with 9 ancestors
2025-12-19 13:28:28,546 - tsinfer.inference - INFO - Finished group 86 of 194 in 0.06 seconds
2025-12-19 13:28:28,547 - tsinfer.inference - INFO - Starting group 87 of 194 with 10 ancestors
2025-12-19 13:28:28,618 - tsinfer.inference - INFO - Finished group 87 of 194 in 0.07 seconds
2025-12-19 13:28:28,619 - tsinfer.inference - INFO - Starting group 88 of 194 with 14 ancestors
2025-12-19 13:28:28,696 - tsinfer.inference - INFO - Finished group 88 of 194 in 0.08 seconds
2025-12-19 13:28:28,698 - tsinfer.inference - INFO - Starting group 89 of 194 with 14 ancestors
2025-12-19 13:28:28,777 - tsinfer.inference - INFO - Finished group 89 of 194 in 0.08 seconds
2025-12-19 13:28:28,779 - tsinfer.inference - INFO - Starting group 90 of 194 with 20 ancestors
2025-12-19 13:28:28,875 - tsinfer.inference - INFO - Finished group 90 of 194 in 0.10 seconds
2025-12-19 13:28:28,876 - tsinfer.inference - INFO - Starting group 91 of 194 with 8 ancestors
2025-12-19 13:28:28,925 - tsinfer.inference - INFO - Finished group 91 of 194 in 0.05 seconds
2025-12-19 13:28:28,927 - tsinfer.inference - INFO - Starting group 92 of 194 with 17 ancestors
2025-12-19 13:28:29,020 - tsinfer.inference - INFO - Finished group 92 of 194 in 0.09 seconds
2025-12-19 13:28:29,021 - tsinfer.inference - INFO - Starting group 93 of 194 with 10 ancestors
2025-12-19 13:28:29,085 - tsinfer.inference - INFO - Finished group 93 of 194 in 0.06 seconds
2025-12-19 13:28:29,087 - tsinfer.inference - INFO - Starting group 94 of 194 with 4 ancestors
2025-12-19 13:28:29,120 - tsinfer.inference - INFO - Finished group 94 of 194 in 0.03 seconds
2025-12-19 13:28:29,121 - tsinfer.inference - INFO - Starting group 95 of 194 with 13 ancestors
2025-12-19 13:28:29,204 - tsinfer.inference - INFO - Finished group 95 of 194 in 0.08 seconds
2025-12-19 13:28:29,205 - tsinfer.inference - INFO - Starting group 96 of 194 with 9 ancestors
2025-12-19 13:28:29,270 - tsinfer.inference - INFO - Finished group 96 of 194 in 0.06 seconds
2025-12-19 13:28:29,271 - tsinfer.inference - INFO - Starting group 97 of 194 with 8 ancestors
2025-12-19 13:28:29,323 - tsinfer.inference - INFO - Finished group 97 of 194 in 0.05 seconds
2025-12-19 13:28:29,323 - tsinfer.inference - INFO - Starting group 98 of 194 with 17 ancestors
2025-12-19 13:28:29,422 - tsinfer.inference - INFO - Finished group 98 of 194 in 0.10 seconds
2025-12-19 13:28:29,424 - tsinfer.inference - INFO - Starting group 99 of 194 with 10 ancestors
2025-12-19 13:28:29,493 - tsinfer.inference - INFO - Finished group 99 of 194 in 0.07 seconds
2025-12-19 13:28:29,495 - tsinfer.inference - INFO - Starting group 100 of 194 with 8 ancestors
2025-12-19 13:28:29,547 - tsinfer.inference - INFO - Finished group 100 of 194 in 0.05 seconds
2025-12-19 13:28:29,548 - tsinfer.inference - INFO - Starting group 101 of 194 with 15 ancestors
2025-12-19 13:28:29,636 - tsinfer.inference - INFO - Finished group 101 of 194 in 0.09 seconds
2025-12-19 13:28:29,637 - tsinfer.inference - INFO - Starting group 102 of 194 with 15 ancestors
2025-12-19 13:28:29,725 - tsinfer.inference - INFO - Finished group 102 of 194 in 0.09 seconds
2025-12-19 13:28:29,727 - tsinfer.inference - INFO - Starting group 103 of 194 with 12 ancestors
2025-12-19 13:28:29,798 - tsinfer.inference - INFO - Finished group 103 of 194 in 0.07 seconds
2025-12-19 13:28:29,800 - tsinfer.inference - INFO - Starting group 104 of 194 with 15 ancestors
2025-12-19 13:28:29,890 - tsinfer.inference - INFO - Finished group 104 of 194 in 0.09 seconds
2025-12-19 13:28:29,892 - tsinfer.inference - INFO - Starting group 105 of 194 with 12 ancestors
2025-12-19 13:28:29,963 - tsinfer.inference - INFO - Finished group 105 of 194 in 0.07 seconds
2025-12-19 13:28:29,964 - tsinfer.inference - INFO - Starting group 106 of 194 with 7 ancestors
2025-12-19 13:28:30,016 - tsinfer.inference - INFO - Finished group 106 of 194 in 0.05 seconds
2025-12-19 13:28:30,018 - tsinfer.inference - INFO - Starting group 107 of 194 with 10 ancestors
2025-12-19 13:28:30,088 - tsinfer.inference - INFO - Finished group 107 of 194 in 0.07 seconds
2025-12-19 13:28:30,090 - tsinfer.inference - INFO - Starting group 108 of 194 with 8 ancestors
2025-12-19 13:28:30,145 - tsinfer.inference - INFO - Finished group 108 of 194 in 0.06 seconds
2025-12-19 13:28:30,147 - tsinfer.inference - INFO - Starting group 109 of 194 with 15 ancestors
2025-12-19 13:28:30,219 - tsinfer.inference - INFO - Finished group 109 of 194 in 0.07 seconds
2025-12-19 13:28:30,220 - tsinfer.inference - INFO - Starting group 110 of 194 with 3 ancestors
2025-12-19 13:28:30,257 - tsinfer.inference - INFO - Finished group 110 of 194 in 0.04 seconds
2025-12-19 13:28:30,257 - tsinfer.inference - INFO - Starting group 111 of 194 with 3 ancestors
2025-12-19 13:28:30,291 - tsinfer.inference - INFO - Finished group 111 of 194 in 0.03 seconds
2025-12-19 13:28:30,292 - tsinfer.inference - INFO - Starting group 112 of 194 with 1 ancestors
2025-12-19 13:28:30,324 - tsinfer.inference - INFO - Finished group 112 of 194 in 0.03 seconds
2025-12-19 13:28:30,325 - tsinfer.inference - INFO - Starting group 113 of 194 with 20 ancestors
2025-12-19 13:28:30,348 - tsinfer.inference - INFO - Finished group 113 of 194 in 0.02 seconds
2025-12-19 13:28:30,350 - tsinfer.inference - INFO - Starting group 114 of 194 with 6 ancestors
2025-12-19 13:28:30,368 - tsinfer.inference - INFO - Finished group 114 of 194 in 0.02 seconds
2025-12-19 13:28:30,369 - tsinfer.inference - INFO - Starting group 115 of 194 with 1 ancestors
2025-12-19 13:28:30,383 - tsinfer.inference - INFO - Finished group 115 of 194 in 0.01 seconds
2025-12-19 13:28:30,384 - tsinfer.inference - INFO - Starting group 116 of 194 with 3 ancestors
2025-12-19 13:28:30,417 - tsinfer.inference - INFO - Finished group 116 of 194 in 0.03 seconds
2025-12-19 13:28:30,418 - tsinfer.inference - INFO - Starting group 117 of 194 with 6 ancestors
2025-12-19 13:28:30,453 - tsinfer.inference - INFO - Finished group 117 of 194 in 0.04 seconds
2025-12-19 13:28:30,454 - tsinfer.inference - INFO - Starting group 118 of 194 with 9 ancestors
2025-12-19 13:28:30,474 - tsinfer.inference - INFO - Finished group 118 of 194 in 0.02 seconds
2025-12-19 13:28:30,475 - tsinfer.inference - INFO - Starting group 119 of 194 with 2 ancestors
2025-12-19 13:28:30,493 - tsinfer.inference - INFO - Finished group 119 of 194 in 0.02 seconds
2025-12-19 13:28:30,494 - tsinfer.inference - INFO - Starting group 120 of 194 with 6 ancestors
2025-12-19 13:28:30,528 - tsinfer.inference - INFO - Finished group 120 of 194 in 0.03 seconds
2025-12-19 13:28:30,530 - tsinfer.inference - INFO - Starting group 121 of 194 with 17 ancestors
2025-12-19 13:28:30,556 - tsinfer.inference - INFO - Finished group 121 of 194 in 0.03 seconds
2025-12-19 13:28:30,558 - tsinfer.inference - INFO - Starting group 122 of 194 with 2 ancestors
2025-12-19 13:28:30,575 - tsinfer.inference - INFO - Finished group 122 of 194 in 0.02 seconds
2025-12-19 13:28:30,576 - tsinfer.inference - INFO - Starting group 123 of 194 with 1 ancestors
2025-12-19 13:28:30,594 - tsinfer.inference - INFO - Finished group 123 of 194 in 0.02 seconds
2025-12-19 13:28:30,595 - tsinfer.inference - INFO - Starting group 124 of 194 with 9 ancestors
2025-12-19 13:28:30,629 - tsinfer.inference - INFO - Finished group 124 of 194 in 0.03 seconds
2025-12-19 13:28:30,632 - tsinfer.inference - INFO - Starting group 125 of 194 with 12 ancestors
2025-12-19 13:28:30,655 - tsinfer.inference - INFO - Finished group 125 of 194 in 0.02 seconds
2025-12-19 13:28:30,656 - tsinfer.inference - INFO - Starting group 126 of 194 with 2 ancestors
2025-12-19 13:28:30,674 - tsinfer.inference - INFO - Finished group 126 of 194 in 0.02 seconds
2025-12-19 13:28:30,675 - tsinfer.inference - INFO - Starting group 127 of 194 with 8 ancestors
2025-12-19 13:28:30,711 - tsinfer.inference - INFO - Finished group 127 of 194 in 0.04 seconds
2025-12-19 13:28:30,712 - tsinfer.inference - INFO - Starting group 128 of 194 with 8 ancestors
2025-12-19 13:28:30,747 - tsinfer.inference - INFO - Finished group 128 of 194 in 0.03 seconds
2025-12-19 13:28:30,748 - tsinfer.inference - INFO - Starting group 129 of 194 with 29 ancestors
2025-12-19 13:28:30,775 - tsinfer.inference - INFO - Finished group 129 of 194 in 0.03 seconds
2025-12-19 13:28:30,777 - tsinfer.inference - INFO - Starting group 130 of 194 with 8 ancestors
2025-12-19 13:28:30,796 - tsinfer.inference - INFO - Finished group 130 of 194 in 0.02 seconds
2025-12-19 13:28:30,797 - tsinfer.inference - INFO - Starting group 131 of 194 with 1 ancestors
2025-12-19 13:28:30,812 - tsinfer.inference - INFO - Finished group 131 of 194 in 0.01 seconds
2025-12-19 13:28:30,814 - tsinfer.inference - INFO - Starting group 132 of 194 with 15 ancestors
2025-12-19 13:28:30,854 - tsinfer.inference - INFO - Finished group 132 of 194 in 0.04 seconds
2025-12-19 13:28:30,856 - tsinfer.inference - INFO - Starting group 133 of 194 with 16 ancestors
2025-12-19 13:28:30,881 - tsinfer.inference - INFO - Finished group 133 of 194 in 0.03 seconds
2025-12-19 13:28:30,883 - tsinfer.inference - INFO - Starting group 134 of 194 with 1 ancestors
2025-12-19 13:28:30,899 - tsinfer.inference - INFO - Finished group 134 of 194 in 0.02 seconds
2025-12-19 13:28:30,901 - tsinfer.inference - INFO - Starting group 135 of 194 with 16 ancestors
2025-12-19 13:28:30,937 - tsinfer.inference - INFO - Finished group 135 of 194 in 0.04 seconds
2025-12-19 13:28:30,938 - tsinfer.inference - INFO - Starting group 136 of 194 with 30 ancestors
2025-12-19 13:28:30,970 - tsinfer.inference - INFO - Finished group 136 of 194 in 0.03 seconds
2025-12-19 13:28:30,972 - tsinfer.inference - INFO - Starting group 137 of 194 with 12 ancestors
2025-12-19 13:28:30,994 - tsinfer.inference - INFO - Finished group 137 of 194 in 0.02 seconds
2025-12-19 13:28:30,995 - tsinfer.inference - INFO - Starting group 138 of 194 with 5 ancestors
2025-12-19 13:28:31,012 - tsinfer.inference - INFO - Finished group 138 of 194 in 0.02 seconds
2025-12-19 13:28:31,013 - tsinfer.inference - INFO - Starting group 139 of 194 with 3 ancestors
2025-12-19 13:28:31,029 - tsinfer.inference - INFO - Finished group 139 of 194 in 0.02 seconds
2025-12-19 13:28:31,030 - tsinfer.inference - INFO - Starting group 140 of 194 with 11 ancestors
2025-12-19 13:28:31,069 - tsinfer.inference - INFO - Finished group 140 of 194 in 0.04 seconds
2025-12-19 13:28:31,071 - tsinfer.inference - INFO - Starting group 141 of 194 with 9 ancestors
2025-12-19 13:28:31,093 - tsinfer.inference - INFO - Finished group 141 of 194 in 0.02 seconds
2025-12-19 13:28:31,095 - tsinfer.inference - INFO - Starting group 142 of 194 with 18 ancestors
2025-12-19 13:28:31,140 - tsinfer.inference - INFO - Finished group 142 of 194 in 0.04 seconds
2025-12-19 13:28:31,141 - tsinfer.inference - INFO - Starting group 143 of 194 with 52 ancestors
2025-12-19 13:28:31,179 - tsinfer.inference - INFO - Finished group 143 of 194 in 0.04 seconds
2025-12-19 13:28:31,181 - tsinfer.inference - INFO - Starting group 144 of 194 with 37 ancestors
2025-12-19 13:28:31,215 - tsinfer.inference - INFO - Finished group 144 of 194 in 0.03 seconds
2025-12-19 13:28:31,216 - tsinfer.inference - INFO - Starting group 145 of 194 with 32 ancestors
2025-12-19 13:28:31,250 - tsinfer.inference - INFO - Finished group 145 of 194 in 0.03 seconds
2025-12-19 13:28:31,252 - tsinfer.inference - INFO - Starting group 146 of 194 with 25 ancestors
2025-12-19 13:28:31,279 - tsinfer.inference - INFO - Finished group 146 of 194 in 0.03 seconds
2025-12-19 13:28:31,281 - tsinfer.inference - INFO - Starting group 147 of 194 with 16 ancestors
2025-12-19 13:28:31,306 - tsinfer.inference - INFO - Finished group 147 of 194 in 0.03 seconds
2025-12-19 13:28:31,308 - tsinfer.inference - INFO - Starting group 148 of 194 with 6 ancestors
2025-12-19 13:28:31,325 - tsinfer.inference - INFO - Finished group 148 of 194 in 0.02 seconds
2025-12-19 13:28:31,326 - tsinfer.inference - INFO - Starting group 149 of 194 with 3 ancestors
2025-12-19 13:28:31,342 - tsinfer.inference - INFO - Finished group 149 of 194 in 0.02 seconds
2025-12-19 13:28:31,344 - tsinfer.inference - INFO - Starting group 150 of 194 with 2 ancestors
2025-12-19 13:28:31,360 - tsinfer.inference - INFO - Finished group 150 of 194 in 0.02 seconds
2025-12-19 13:28:31,361 - tsinfer.inference - INFO - Starting group 151 of 194 with 11 ancestors
2025-12-19 13:28:31,408 - tsinfer.inference - INFO - Finished group 151 of 194 in 0.05 seconds
2025-12-19 13:28:31,409 - tsinfer.inference - INFO - Starting group 152 of 194 with 18 ancestors
2025-12-19 13:28:31,454 - tsinfer.inference - INFO - Finished group 152 of 194 in 0.05 seconds
2025-12-19 13:28:31,455 - tsinfer.inference - INFO - Starting group 153 of 194 with 17 ancestors
2025-12-19 13:28:31,501 - tsinfer.inference - INFO - Finished group 153 of 194 in 0.05 seconds
2025-12-19 13:28:31,503 - tsinfer.inference - INFO - Starting group 154 of 194 with 44 ancestors
2025-12-19 13:28:31,542 - tsinfer.inference - INFO - Finished group 154 of 194 in 0.04 seconds
2025-12-19 13:28:31,544 - tsinfer.inference - INFO - Starting group 155 of 194 with 41 ancestors
2025-12-19 13:28:31,581 - tsinfer.inference - INFO - Finished group 155 of 194 in 0.04 seconds
2025-12-19 13:28:31,582 - tsinfer.inference - INFO - Starting group 156 of 194 with 18 ancestors
2025-12-19 13:28:31,607 - tsinfer.inference - INFO - Finished group 156 of 194 in 0.03 seconds
2025-12-19 13:28:31,609 - tsinfer.inference - INFO - Starting group 157 of 194 with 3 ancestors
2025-12-19 13:28:31,626 - tsinfer.inference - INFO - Finished group 157 of 194 in 0.02 seconds
2025-12-19 13:28:31,627 - tsinfer.inference - INFO - Starting group 158 of 194 with 23 ancestors
2025-12-19 13:28:31,667 - tsinfer.inference - INFO - Finished group 158 of 194 in 0.04 seconds
2025-12-19 13:28:31,667 - tsinfer.inference - INFO - Starting group 159 of 194 with 29 ancestors
2025-12-19 13:28:31,711 - tsinfer.inference - INFO - Finished group 159 of 194 in 0.04 seconds
2025-12-19 13:28:31,713 - tsinfer.inference - INFO - Starting group 160 of 194 with 32 ancestors
2025-12-19 13:28:31,747 - tsinfer.inference - INFO - Finished group 160 of 194 in 0.03 seconds
2025-12-19 13:28:31,748 - tsinfer.inference - INFO - Starting group 161 of 194 with 24 ancestors
2025-12-19 13:28:31,778 - tsinfer.inference - INFO - Finished group 161 of 194 in 0.03 seconds
2025-12-19 13:28:31,779 - tsinfer.inference - INFO - Starting group 162 of 194 with 6 ancestors
2025-12-19 13:28:31,799 - tsinfer.inference - INFO - Finished group 162 of 194 in 0.02 seconds
2025-12-19 13:28:31,800 - tsinfer.inference - INFO - Starting group 163 of 194 with 32 ancestors
2025-12-19 13:28:31,862 - tsinfer.inference - INFO - Finished group 163 of 194 in 0.06 seconds
2025-12-19 13:28:31,864 - tsinfer.inference - INFO - Starting group 164 of 194 with 34 ancestors
2025-12-19 13:28:31,909 - tsinfer.inference - INFO - Finished group 164 of 194 in 0.05 seconds
2025-12-19 13:28:31,911 - tsinfer.inference - INFO - Starting group 165 of 194 with 16 ancestors
2025-12-19 13:28:31,936 - tsinfer.inference - INFO - Finished group 165 of 194 in 0.02 seconds
2025-12-19 13:28:31,936 - tsinfer.inference - INFO - Starting group 166 of 194 with 39 ancestors
2025-12-19 13:28:31,981 - tsinfer.inference - INFO - Finished group 166 of 194 in 0.04 seconds
2025-12-19 13:28:31,981 - tsinfer.inference - INFO - Starting group 167 of 194 with 44 ancestors
2025-12-19 13:28:32,024 - tsinfer.inference - INFO - Finished group 167 of 194 in 0.04 seconds
2025-12-19 13:28:32,025 - tsinfer.inference - INFO - Starting group 168 of 194 with 29 ancestors
2025-12-19 13:28:32,070 - tsinfer.inference - INFO - Finished group 168 of 194 in 0.05 seconds
2025-12-19 13:28:32,071 - tsinfer.inference - INFO - Starting group 169 of 194 with 45 ancestors
2025-12-19 13:28:32,111 - tsinfer.inference - INFO - Finished group 169 of 194 in 0.04 seconds
2025-12-19 13:28:32,113 - tsinfer.inference - INFO - Starting group 170 of 194 with 25 ancestors
2025-12-19 13:28:32,142 - tsinfer.inference - INFO - Finished group 170 of 194 in 0.03 seconds
2025-12-19 13:28:32,144 - tsinfer.inference - INFO - Starting group 171 of 194 with 48 ancestors
2025-12-19 13:28:32,205 - tsinfer.inference - INFO - Finished group 171 of 194 in 0.06 seconds
2025-12-19 13:28:32,207 - tsinfer.inference - INFO - Starting group 172 of 194 with 31 ancestors
2025-12-19 13:28:32,245 - tsinfer.inference - INFO - Finished group 172 of 194 in 0.04 seconds
2025-12-19 13:28:32,247 - tsinfer.inference - INFO - Starting group 173 of 194 with 52 ancestors
2025-12-19 13:28:32,311 - tsinfer.inference - INFO - Finished group 173 of 194 in 0.06 seconds
2025-12-19 13:28:32,313 - tsinfer.inference - INFO - Starting group 174 of 194 with 54 ancestors
2025-12-19 13:28:32,358 - tsinfer.inference - INFO - Finished group 174 of 194 in 0.04 seconds
2025-12-19 13:28:32,359 - tsinfer.inference - INFO - Starting group 175 of 194 with 62 ancestors
2025-12-19 13:28:32,413 - tsinfer.inference - INFO - Finished group 175 of 194 in 0.05 seconds
2025-12-19 13:28:32,415 - tsinfer.inference - INFO - Starting group 176 of 194 with 41 ancestors
2025-12-19 13:28:32,455 - tsinfer.inference - INFO - Finished group 176 of 194 in 0.04 seconds
2025-12-19 13:28:32,456 - tsinfer.inference - INFO - Starting group 177 of 194 with 53 ancestors
2025-12-19 13:28:32,509 - tsinfer.inference - INFO - Finished group 177 of 194 in 0.05 seconds
2025-12-19 13:28:32,510 - tsinfer.inference - INFO - Starting group 178 of 194 with 92 ancestors
2025-12-19 13:28:32,576 - tsinfer.inference - INFO - Finished group 178 of 194 in 0.07 seconds
2025-12-19 13:28:32,577 - tsinfer.inference - INFO - Starting group 179 of 194 with 81 ancestors
2025-12-19 13:28:32,638 - tsinfer.inference - INFO - Finished group 179 of 194 in 0.06 seconds
2025-12-19 13:28:32,639 - tsinfer.inference - INFO - Starting group 180 of 194 with 78 ancestors
2025-12-19 13:28:32,703 - tsinfer.inference - INFO - Finished group 180 of 194 in 0.06 seconds
2025-12-19 13:28:32,704 - tsinfer.inference - INFO - Starting group 181 of 194 with 82 ancestors
2025-12-19 13:28:32,770 - tsinfer.inference - INFO - Finished group 181 of 194 in 0.07 seconds
2025-12-19 13:28:32,771 - tsinfer.inference - INFO - Starting group 182 of 194 with 110 ancestors
2025-12-19 13:28:32,861 - tsinfer.inference - INFO - Finished group 182 of 194 in 0.09 seconds
2025-12-19 13:28:32,862 - tsinfer.inference - INFO - Starting group 183 of 194 with 103 ancestors
2025-12-19 13:28:32,948 - tsinfer.inference - INFO - Finished group 183 of 194 in 0.09 seconds
2025-12-19 13:28:32,949 - tsinfer.inference - INFO - Starting group 184 of 194 with 119 ancestors
2025-12-19 13:28:33,031 - tsinfer.inference - INFO - Finished group 184 of 194 in 0.08 seconds
2025-12-19 13:28:33,032 - tsinfer.inference - INFO - Starting group 185 of 194 with 128 ancestors
2025-12-19 13:28:33,140 - tsinfer.inference - INFO - Finished group 185 of 194 in 0.11 seconds
2025-12-19 13:28:33,141 - tsinfer.inference - INFO - Starting group 186 of 194 with 166 ancestors
2025-12-19 13:28:33,271 - tsinfer.inference - INFO - Finished group 186 of 194 in 0.13 seconds
2025-12-19 13:28:33,272 - tsinfer.inference - INFO - Starting group 187 of 194 with 176 ancestors
2025-12-19 13:28:33,414 - tsinfer.inference - INFO - Finished group 187 of 194 in 0.14 seconds
2025-12-19 13:28:33,415 - tsinfer.inference - INFO - Starting group 188 of 194 with 199 ancestors
2025-12-19 13:28:33,570 - tsinfer.inference - INFO - Finished group 188 of 194 in 0.16 seconds
2025-12-19 13:28:33,571 - tsinfer.inference - INFO - Starting group 189 of 194 with 272 ancestors
2025-12-19 13:28:33,775 - tsinfer.inference - INFO - Finished group 189 of 194 in 0.20 seconds
2025-12-19 13:28:33,776 - tsinfer.inference - INFO - Starting group 190 of 194 with 332 ancestors
2025-12-19 13:28:34,033 - tsinfer.inference - INFO - Finished group 190 of 194 in 0.26 seconds
2025-12-19 13:28:34,035 - tsinfer.inference - INFO - Starting group 191 of 194 with 438 ancestors
2025-12-19 13:28:34,426 - tsinfer.inference - INFO - Finished group 191 of 194 in 0.39 seconds
2025-12-19 13:28:34,427 - tsinfer.inference - INFO - Starting group 192 of 194 with 666 ancestors
2025-12-19 13:28:35,032 - tsinfer.inference - INFO - Finished group 192 of 194 in 0.60 seconds
2025-12-19 13:28:35,033 - tsinfer.inference - INFO - Starting group 193 of 194 with 795 ancestors
2025-12-19 13:28:35,734 - tsinfer.inference - INFO - Finished group 193 of 194 in 0.70 seconds
2025-12-19 13:28:35,860 - tsinfer.inference - INFO - Built ancestors tree sequence: 6991 nodes (520 pc ancestors); 29013 edges; 8605 sites; 8605 mutations
2025-12-19 13:28:35,863 - tsinfer.inference - INFO - Finished ancestor matching
2025-12-19 13:28:35,884 - tsinfer.inference - INFO - Mismatch prevented by setting constant high recombination and low mismatch probabilities
2025-12-19 13:28:35,885 - tsinfer.inference - INFO - Summary of recombination probabilities between sites: min=0.01; max=0.01; median=0.01; mean=0.01
2025-12-19 13:28:35,886 - tsinfer.inference - INFO - Summary of mismatch probabilities over sites: min=1e-20; max=1e-20; median=1e-20; mean=1e-20
2025-12-19 13:28:35,887 - tsinfer.inference - INFO - Matching using likelihood_threshold of 1e-13
2025-12-19 13:28:36,006 - tsinfer.inference - INFO - Loaded 210 samples 6991 nodes; 29013 edges; 8605 sites; 8605 mutations
2025-12-19 13:28:36,008 - tsinfer.inference - INFO - Started matching for 210 samples
2025-12-19 13:28:36,016 - tsinfer.inference - INFO - 1766147316.0166554Thread 139778829837888 starting haplotype 0
2025-12-19 13:28:36,019 - tsinfer.inference - INFO - 1766147316.0193193Thread 139778916025920 starting haplotype 1
2025-12-19 13:28:36,021 - tsinfer.inference - INFO - 1766147316.021852Thread 139778821445184 starting haplotype 2
2025-12-19 13:28:36,024 - tsinfer.inference - INFO - 1766147316.0245705Thread 139778838230592 starting haplotype 3
2025-12-19 13:28:36,043 - tsinfer.inference - INFO - 1766147316.0431087Thread 139778829837888 finished haplotype 0
2025-12-19 13:28:36,044 - tsinfer.inference - INFO - 1766147316.0446036Thread 139778829837888 starting haplotype 4
2025-12-19 13:28:36,047 - tsinfer.inference - INFO - 1766147316.047745Thread 139778916025920 finished haplotype 1
2025-12-19 13:28:36,049 - tsinfer.inference - INFO - 1766147316.0497096Thread 139778916025920 starting haplotype 5
2025-12-19 13:28:36,051 - tsinfer.inference - INFO - 1766147316.0511224Thread 139778821445184 finished haplotype 2
2025-12-19 13:28:36,052 - tsinfer.inference - INFO - 1766147316.0524318Thread 139778838230592 finished haplotype 3
2025-12-19 13:28:36,052 - tsinfer.inference - INFO - 1766147316.0528095Thread 139778821445184 starting haplotype 6
2025-12-19 13:28:36,054 - tsinfer.inference - INFO - 1766147316.0542974Thread 139778838230592 starting haplotype 7
2025-12-19 13:28:36,071 - tsinfer.inference - INFO - 1766147316.071712Thread 139778829837888 finished haplotype 4
2025-12-19 13:28:36,072 - tsinfer.inference - INFO - 1766147316.0724323Thread 139778829837888 starting haplotype 8
2025-12-19 13:28:36,080 - tsinfer.inference - INFO - 1766147316.0804048Thread 139778916025920 finished haplotype 5
2025-12-19 13:28:36,081 - tsinfer.inference - INFO - 1766147316.08115Thread 139778916025920 starting haplotype 9
2025-12-19 13:28:36,085 - tsinfer.inference - INFO - 1766147316.0853925Thread 139778838230592 finished haplotype 7
2025-12-19 13:28:36,086 - tsinfer.inference - INFO - 1766147316.0864007Thread 139778838230592 starting haplotype 10
2025-12-19 13:28:36,088 - tsinfer.inference - INFO - 1766147316.0883787Thread 139778821445184 finished haplotype 6
2025-12-19 13:28:36,089 - tsinfer.inference - INFO - 1766147316.089894Thread 139778821445184 starting haplotype 11
2025-12-19 13:28:36,099 - tsinfer.inference - INFO - 1766147316.0994768Thread 139778829837888 finished haplotype 8
2025-12-19 13:28:36,100 - tsinfer.inference - INFO - 1766147316.1009622Thread 139778829837888 starting haplotype 12
2025-12-19 13:28:36,108 - tsinfer.inference - INFO - 1766147316.1085901Thread 139778916025920 finished haplotype 9
2025-12-19 13:28:36,110 - tsinfer.inference - INFO - 1766147316.1102643Thread 139778916025920 starting haplotype 13
2025-12-19 13:28:36,113 - tsinfer.inference - INFO - 1766147316.113868Thread 139778838230592 finished haplotype 10
2025-12-19 13:28:36,115 - tsinfer.inference - INFO - 1766147316.1154861Thread 139778838230592 starting haplotype 14
2025-12-19 13:28:36,120 - tsinfer.inference - INFO - 1766147316.1205783Thread 139778821445184 finished haplotype 11
2025-12-19 13:28:36,122 - tsinfer.inference - INFO - 1766147316.1220174Thread 139778821445184 starting haplotype 15
2025-12-19 13:28:36,127 - tsinfer.inference - INFO - 1766147316.1278474Thread 139778829837888 finished haplotype 12
2025-12-19 13:28:36,129 - tsinfer.inference - INFO - 1766147316.1293027Thread 139778829837888 starting haplotype 16
2025-12-19 13:28:36,137 - tsinfer.inference - INFO - 1766147316.1377418Thread 139778916025920 finished haplotype 13
2025-12-19 13:28:36,139 - tsinfer.inference - INFO - 1766147316.139385Thread 139778916025920 starting haplotype 17
2025-12-19 13:28:36,142 - tsinfer.inference - INFO - 1766147316.1429462Thread 139778838230592 finished haplotype 14
2025-12-19 13:28:36,144 - tsinfer.inference - INFO - 1766147316.1446717Thread 139778838230592 starting haplotype 18
2025-12-19 13:28:36,149 - tsinfer.inference - INFO - 1766147316.14904Thread 139778821445184 finished haplotype 15
2025-12-19 13:28:36,150 - tsinfer.inference - INFO - 1766147316.150478Thread 139778821445184 starting haplotype 19
2025-12-19 13:28:36,156 - tsinfer.inference - INFO - 1766147316.1562867Thread 139778829837888 finished haplotype 16
2025-12-19 13:28:36,157 - tsinfer.inference - INFO - 1766147316.1577225Thread 139778829837888 starting haplotype 20
2025-12-19 13:28:36,166 - tsinfer.inference - INFO - 1766147316.1661866Thread 139778916025920 finished haplotype 17
2025-12-19 13:28:36,167 - tsinfer.inference - INFO - 1766147316.1677976Thread 139778916025920 starting haplotype 21
2025-12-19 13:28:36,172 - tsinfer.inference - INFO - 1766147316.1724877Thread 139778838230592 finished haplotype 18
2025-12-19 13:28:36,174 - tsinfer.inference - INFO - 1766147316.1742141Thread 139778838230592 starting haplotype 22
2025-12-19 13:28:36,178 - tsinfer.inference - INFO - 1766147316.1779842Thread 139778821445184 finished haplotype 19
2025-12-19 13:28:36,179 - tsinfer.inference - INFO - 1766147316.1794107Thread 139778821445184 starting haplotype 23
2025-12-19 13:28:36,184 - tsinfer.inference - INFO - 1766147316.184339Thread 139778829837888 finished haplotype 20
2025-12-19 13:28:36,185 - tsinfer.inference - INFO - 1766147316.1851416Thread 139778829837888 starting haplotype 24
2025-12-19 13:28:36,195 - tsinfer.inference - INFO - 1766147316.195743Thread 139778916025920 finished haplotype 21
2025-12-19 13:28:36,196 - tsinfer.inference - INFO - 1766147316.1966412Thread 139778916025920 starting haplotype 25
2025-12-19 13:28:36,202 - tsinfer.inference - INFO - 1766147316.2029207Thread 139778838230592 finished haplotype 22
2025-12-19 13:28:36,203 - tsinfer.inference - INFO - 1766147316.2038634Thread 139778838230592 starting haplotype 26
2025-12-19 13:28:36,209 - tsinfer.inference - INFO - 1766147316.2093604Thread 139778821445184 finished haplotype 23
2025-12-19 13:28:36,210 - tsinfer.inference - INFO - 1766147316.210823Thread 139778821445184 starting haplotype 27
2025-12-19 13:28:36,212 - tsinfer.inference - INFO - 1766147316.2121615Thread 139778829837888 finished haplotype 24
2025-12-19 13:28:36,214 - tsinfer.inference - INFO - 1766147316.2140043Thread 139778829837888 starting haplotype 28
2025-12-19 13:28:36,223 - tsinfer.inference - INFO - 1766147316.2232225Thread 139778916025920 finished haplotype 25
2025-12-19 13:28:36,224 - tsinfer.inference - INFO - 1766147316.2248461Thread 139778916025920 starting haplotype 29
2025-12-19 13:28:36,231 - tsinfer.inference - INFO - 1766147316.2310748Thread 139778838230592 finished haplotype 26
2025-12-19 13:28:36,232 - tsinfer.inference - INFO - 1766147316.2326329Thread 139778838230592 starting haplotype 30
2025-12-19 13:28:36,237 - tsinfer.inference - INFO - 1766147316.2378516Thread 139778821445184 finished haplotype 27
2025-12-19 13:28:36,238 - tsinfer.inference - INFO - 1766147316.238654Thread 139778821445184 starting haplotype 31
2025-12-19 13:28:36,243 - tsinfer.inference - INFO - 1766147316.2438827Thread 139778829837888 finished haplotype 28
2025-12-19 13:28:36,244 - tsinfer.inference - INFO - 1766147316.2446742Thread 139778829837888 starting haplotype 32
2025-12-19 13:28:36,250 - tsinfer.inference - INFO - 1766147316.2506926Thread 139778916025920 finished haplotype 29
2025-12-19 13:28:36,251 - tsinfer.inference - INFO - 1766147316.2515857Thread 139778916025920 starting haplotype 33
2025-12-19 13:28:36,263 - tsinfer.inference - INFO - 1766147316.2632017Thread 139778838230592 finished haplotype 30
2025-12-19 13:28:36,264 - tsinfer.inference - INFO - 1766147316.264831Thread 139778838230592 starting haplotype 34
2025-12-19 13:28:36,266 - tsinfer.inference - INFO - 1766147316.266332Thread 139778821445184 finished haplotype 31
2025-12-19 13:28:36,267 - tsinfer.inference - INFO - 1766147316.2672908Thread 139778821445184 starting haplotype 35
2025-12-19 13:28:36,270 - tsinfer.inference - INFO - 1766147316.2708812Thread 139778829837888 finished haplotype 32
2025-12-19 13:28:36,271 - tsinfer.inference - INFO - 1766147316.2716804Thread 139778829837888 starting haplotype 36
2025-12-19 13:28:36,278 - tsinfer.inference - INFO - 1766147316.2781072Thread 139778916025920 finished haplotype 33
2025-12-19 13:28:36,279 - tsinfer.inference - INFO - 1766147316.2789922Thread 139778916025920 starting haplotype 37
2025-12-19 13:28:36,293 - tsinfer.inference - INFO - 1766147316.2933276Thread 139778821445184 finished haplotype 35
2025-12-19 13:28:36,294 - tsinfer.inference - INFO - 1766147316.29425Thread 139778821445184 starting haplotype 38
2025-12-19 13:28:36,297 - tsinfer.inference - INFO - 1766147316.2974885Thread 139778838230592 finished haplotype 34
2025-12-19 13:28:36,298 - tsinfer.inference - INFO - 1766147316.2981539Thread 139778829837888 finished haplotype 36
2025-12-19 13:28:36,299 - tsinfer.inference - INFO - 1766147316.2990384Thread 139778838230592 starting haplotype 39
2025-12-19 13:28:36,301 - tsinfer.inference - INFO - 1766147316.301064Thread 139778829837888 starting haplotype 40
2025-12-19 13:28:36,306 - tsinfer.inference - INFO - 1766147316.3062286Thread 139778916025920 finished haplotype 37
2025-12-19 13:28:36,307 - tsinfer.inference - INFO - 1766147316.307764Thread 139778916025920 starting haplotype 41
2025-12-19 13:28:36,320 - tsinfer.inference - INFO - 1766147316.3208008Thread 139778821445184 finished haplotype 38
2025-12-19 13:28:36,322 - tsinfer.inference - INFO - 1766147316.3222847Thread 139778821445184 starting haplotype 42
2025-12-19 13:28:36,328 - tsinfer.inference - INFO - 1766147316.3281765Thread 139778838230592 finished haplotype 39
2025-12-19 13:28:36,329 - tsinfer.inference - INFO - 1766147316.329789Thread 139778838230592 starting haplotype 43
2025-12-19 13:28:36,332 - tsinfer.inference - INFO - 1766147316.3326724Thread 139778829837888 finished haplotype 40
2025-12-19 13:28:36,334 - tsinfer.inference - INFO - 1766147316.3342037Thread 139778829837888 starting haplotype 44
2025-12-19 13:28:36,337 - tsinfer.inference - INFO - 1766147316.3371673Thread 139778916025920 finished haplotype 41
2025-12-19 13:28:36,338 - tsinfer.inference - INFO - 1766147316.3380315Thread 139778916025920 starting haplotype 45
2025-12-19 13:28:36,349 - tsinfer.inference - INFO - 1766147316.3493087Thread 139778821445184 finished haplotype 42
2025-12-19 13:28:36,350 - tsinfer.inference - INFO - 1766147316.3502483Thread 139778821445184 starting haplotype 46
2025-12-19 13:28:36,357 - tsinfer.inference - INFO - 1766147316.3575842Thread 139778838230592 finished haplotype 43
2025-12-19 13:28:36,358 - tsinfer.inference - INFO - 1766147316.3584538Thread 139778838230592 starting haplotype 47
2025-12-19 13:28:36,364 - tsinfer.inference - INFO - 1766147316.3642573Thread 139778916025920 finished haplotype 45
2025-12-19 13:28:36,365 - tsinfer.inference - INFO - 1766147316.3650029Thread 139778829837888 finished haplotype 44
2025-12-19 13:28:36,366 - tsinfer.inference - INFO - 1766147316.366076Thread 139778916025920 starting haplotype 48
2025-12-19 13:28:36,367 - tsinfer.inference - INFO - 1766147316.3679507Thread 139778829837888 starting haplotype 49
2025-12-19 13:28:36,376 - tsinfer.inference - INFO - 1766147316.3764732Thread 139778821445184 finished haplotype 46
2025-12-19 13:28:36,377 - tsinfer.inference - INFO - 1766147316.3772938Thread 139778821445184 starting haplotype 50
2025-12-19 13:28:36,385 - tsinfer.inference - INFO - 1766147316.3853Thread 139778838230592 finished haplotype 47
2025-12-19 13:28:36,386 - tsinfer.inference - INFO - 1766147316.3862128Thread 139778838230592 starting haplotype 51
2025-12-19 13:28:36,396 - tsinfer.inference - INFO - 1766147316.3966649Thread 139778916025920 finished haplotype 48
2025-12-19 13:28:36,397 - tsinfer.inference - INFO - 1766147316.3975866Thread 139778916025920 starting haplotype 52
2025-12-19 13:28:36,401 - tsinfer.inference - INFO - 1766147316.4018586Thread 139778829837888 finished haplotype 49
2025-12-19 13:28:36,403 - tsinfer.inference - INFO - 1766147316.4034698Thread 139778829837888 starting haplotype 53
2025-12-19 13:28:36,404 - tsinfer.inference - INFO - 1766147316.404816Thread 139778821445184 finished haplotype 50
2025-12-19 13:28:36,407 - tsinfer.inference - INFO - 1766147316.4070928Thread 139778821445184 starting haplotype 54
2025-12-19 13:28:36,413 - tsinfer.inference - INFO - 1766147316.4130282Thread 139778838230592 finished haplotype 51
2025-12-19 13:28:36,414 - tsinfer.inference - INFO - 1766147316.4145632Thread 139778838230592 starting haplotype 55
2025-12-19 13:28:36,425 - tsinfer.inference - INFO - 1766147316.425101Thread 139778916025920 finished haplotype 52
2025-12-19 13:28:36,426 - tsinfer.inference - INFO - 1766147316.4265914Thread 139778916025920 starting haplotype 56
2025-12-19 13:28:36,431 - tsinfer.inference - INFO - 1766147316.4315038Thread 139778829837888 finished haplotype 53
2025-12-19 13:28:36,433 - tsinfer.inference - INFO - 1766147316.4331994Thread 139778829837888 starting haplotype 57
2025-12-19 13:28:36,434 - tsinfer.inference - INFO - 1766147316.4346886Thread 139778821445184 finished haplotype 54
2025-12-19 13:28:36,435 - tsinfer.inference - INFO - 1766147316.435526Thread 139778821445184 starting haplotype 58
2025-12-19 13:28:36,441 - tsinfer.inference - INFO - 1766147316.4416425Thread 139778838230592 finished haplotype 55
2025-12-19 13:28:36,442 - tsinfer.inference - INFO - 1766147316.442487Thread 139778838230592 starting haplotype 59
2025-12-19 13:28:36,455 - tsinfer.inference - INFO - 1766147316.4555953Thread 139778916025920 finished haplotype 56
2025-12-19 13:28:36,456 - tsinfer.inference - INFO - 1766147316.456413Thread 139778916025920 starting haplotype 60
2025-12-19 13:28:36,463 - tsinfer.inference - INFO - 1766147316.463305Thread 139778821445184 finished haplotype 58
2025-12-19 13:28:36,464 - tsinfer.inference - INFO - 1766147316.4641013Thread 139778821445184 starting haplotype 61
2025-12-19 13:28:36,465 - tsinfer.inference - INFO - 1766147316.4657223Thread 139778829837888 finished haplotype 57
2025-12-19 13:28:36,467 - tsinfer.inference - INFO - 1766147316.46749Thread 139778829837888 starting haplotype 62
2025-12-19 13:28:36,470 - tsinfer.inference - INFO - 1766147316.470072Thread 139778838230592 finished haplotype 59
2025-12-19 13:28:36,471 - tsinfer.inference - INFO - 1766147316.4718823Thread 139778838230592 starting haplotype 63
2025-12-19 13:28:36,482 - tsinfer.inference - INFO - 1766147316.4828537Thread 139778916025920 finished haplotype 60
2025-12-19 13:28:36,484 - tsinfer.inference - INFO - 1766147316.4843364Thread 139778916025920 starting haplotype 64
2025-12-19 13:28:36,491 - tsinfer.inference - INFO - 1766147316.4914846Thread 139778821445184 finished haplotype 61
2025-12-19 13:28:36,492 - tsinfer.inference - INFO - 1766147316.4929209Thread 139778821445184 starting haplotype 65
2025-12-19 13:28:36,495 - tsinfer.inference - INFO - 1766147316.495158Thread 139778829837888 finished haplotype 62
2025-12-19 13:28:36,496 - tsinfer.inference - INFO - 1766147316.4960604Thread 139778829837888 starting haplotype 66
2025-12-19 13:28:36,499 - tsinfer.inference - INFO - 1766147316.4996166Thread 139778838230592 finished haplotype 63
2025-12-19 13:28:36,500 - tsinfer.inference - INFO - 1766147316.500608Thread 139778838230592 starting haplotype 67
2025-12-19 13:28:36,512 - tsinfer.inference - INFO - 1766147316.5126336Thread 139778916025920 finished haplotype 64
2025-12-19 13:28:36,513 - tsinfer.inference - INFO - 1766147316.5134418Thread 139778916025920 starting haplotype 68
2025-12-19 13:28:36,523 - tsinfer.inference - INFO - 1766147316.5234132Thread 139778821445184 finished haplotype 65
2025-12-19 13:28:36,524 - tsinfer.inference - INFO - 1766147316.524734Thread 139778821445184 starting haplotype 69
2025-12-19 13:28:36,527 - tsinfer.inference - INFO - 1766147316.5271792Thread 139778838230592 finished haplotype 67
2025-12-19 13:28:36,527 - tsinfer.inference - INFO - 1766147316.5278764Thread 139778838230592 starting haplotype 70
2025-12-19 13:28:36,525 - tsinfer.inference - INFO - 1766147316.5254464Thread 139778829837888 finished haplotype 66
2025-12-19 13:28:36,541 - tsinfer.inference - INFO - 1766147316.5418558Thread 139778829837888 starting haplotype 71
2025-12-19 13:28:36,543 - tsinfer.inference - INFO - 1766147316.5438933Thread 139778916025920 finished haplotype 68
2025-12-19 13:28:36,544 - tsinfer.inference - INFO - 1766147316.5445428Thread 139778916025920 starting haplotype 72
2025-12-19 13:28:36,552 - tsinfer.inference - INFO - 1766147316.5528686Thread 139778821445184 finished haplotype 69
2025-12-19 13:28:36,553 - tsinfer.inference - INFO - 1766147316.5537653Thread 139778821445184 starting haplotype 73
2025-12-19 13:28:36,555 - tsinfer.inference - INFO - 1766147316.555012Thread 139778838230592 finished haplotype 70
2025-12-19 13:28:36,556 - tsinfer.inference - INFO - 1766147316.5560167Thread 139778838230592 starting haplotype 74
2025-12-19 13:28:36,571 - tsinfer.inference - INFO - 1766147316.571021Thread 139778916025920 finished haplotype 72
2025-12-19 13:28:36,571 - tsinfer.inference - INFO - 1766147316.5717652Thread 139778916025920 starting haplotype 75
2025-12-19 13:28:36,575 - tsinfer.inference - INFO - 1766147316.5755613Thread 139778829837888 finished haplotype 71
2025-12-19 13:28:36,577 - tsinfer.inference - INFO - 1766147316.57705Thread 139778829837888 starting haplotype 76
2025-12-19 13:28:36,581 - tsinfer.inference - INFO - 1766147316.581882Thread 139778821445184 finished haplotype 73
2025-12-19 13:28:36,582 - tsinfer.inference - INFO - 1766147316.5821967Thread 139778838230592 finished haplotype 74
2025-12-19 13:28:36,582 - tsinfer.inference - INFO - 1766147316.5828066Thread 139778821445184 starting haplotype 77
2025-12-19 13:28:36,584 - tsinfer.inference - INFO - 1766147316.5842729Thread 139778838230592 starting haplotype 78
2025-12-19 13:28:36,598 - tsinfer.inference - INFO - 1766147316.5982232Thread 139778916025920 finished haplotype 75
2025-12-19 13:28:36,599 - tsinfer.inference - INFO - 1766147316.599829Thread 139778916025920 starting haplotype 79
2025-12-19 13:28:36,604 - tsinfer.inference - INFO - 1766147316.6045947Thread 139778829837888 finished haplotype 76
2025-12-19 13:28:36,606 - tsinfer.inference - INFO - 1766147316.6061323Thread 139778829837888 starting haplotype 80
2025-12-19 13:28:36,611 - tsinfer.inference - INFO - 1766147316.611859Thread 139778821445184 finished haplotype 77
2025-12-19 13:28:36,613 - tsinfer.inference - INFO - 1766147316.613478Thread 139778838230592 finished haplotype 78
2025-12-19 13:28:36,613 - tsinfer.inference - INFO - 1766147316.6137602Thread 139778821445184 starting haplotype 81
2025-12-19 13:28:36,615 - tsinfer.inference - INFO - 1766147316.615464Thread 139778838230592 starting haplotype 82
2025-12-19 13:28:36,626 - tsinfer.inference - INFO - 1766147316.6269264Thread 139778916025920 finished haplotype 79
2025-12-19 13:28:36,628 - tsinfer.inference - INFO - 1766147316.6285136Thread 139778916025920 starting haplotype 83
2025-12-19 13:28:36,633 - tsinfer.inference - INFO - 1766147316.6336763Thread 139778829837888 finished haplotype 80
2025-12-19 13:28:36,636 - tsinfer.inference - INFO - 1766147316.6360123Thread 139778829837888 starting haplotype 84
2025-12-19 13:28:36,644 - tsinfer.inference - INFO - 1766147316.6439977Thread 139778838230592 finished haplotype 82
2025-12-19 13:28:36,644 - tsinfer.inference - INFO - 1766147316.6447535Thread 139778821445184 finished haplotype 81
2025-12-19 13:28:36,645 - tsinfer.inference - INFO - 1766147316.6454763Thread 139778838230592 starting haplotype 85
2025-12-19 13:28:36,647 - tsinfer.inference - INFO - 1766147316.6477315Thread 139778821445184 starting haplotype 86
2025-12-19 13:28:36,656 - tsinfer.inference - INFO - 1766147316.6563737Thread 139778916025920 finished haplotype 83
2025-12-19 13:28:36,658 - tsinfer.inference - INFO - 1766147316.6580756Thread 139778916025920 starting haplotype 87
2025-12-19 13:28:36,664 - tsinfer.inference - INFO - 1766147316.664468Thread 139778829837888 finished haplotype 84
2025-12-19 13:28:36,665 - tsinfer.inference - INFO - 1766147316.665331Thread 139778829837888 starting haplotype 88
2025-12-19 13:28:36,677 - tsinfer.inference - INFO - 1766147316.677911Thread 139778821445184 finished haplotype 86
2025-12-19 13:28:36,678 - tsinfer.inference - INFO - 1766147316.6787453Thread 139778838230592 finished haplotype 85
2025-12-19 13:28:36,679 - tsinfer.inference - INFO - 1766147316.6797416Thread 139778821445184 starting haplotype 89
2025-12-19 13:28:36,685 - tsinfer.inference - INFO - 1766147316.6852036Thread 139778916025920 finished haplotype 87
2025-12-19 13:28:36,685 - tsinfer.inference - INFO - 1766147316.6859708Thread 139778916025920 starting haplotype 91
2025-12-19 13:28:36,681 - tsinfer.inference - INFO - 1766147316.6810918Thread 139778838230592 starting haplotype 90
2025-12-19 13:28:36,693 - tsinfer.inference - INFO - 1766147316.693508Thread 139778829837888 finished haplotype 88
2025-12-19 13:28:36,694 - tsinfer.inference - INFO - 1766147316.6944718Thread 139778829837888 starting haplotype 92
2025-12-19 13:28:36,712 - tsinfer.inference - INFO - 1766147316.7120528Thread 139778821445184 finished haplotype 89
2025-12-19 13:28:36,712 - tsinfer.inference - INFO - 1766147316.7128863Thread 139778821445184 starting haplotype 93
2025-12-19 13:28:36,714 - tsinfer.inference - INFO - 1766147316.714029Thread 139778916025920 finished haplotype 91
2025-12-19 13:28:36,715 - tsinfer.inference - INFO - 1766147316.7149878Thread 139778916025920 starting haplotype 94
2025-12-19 13:28:36,719 - tsinfer.inference - INFO - 1766147316.7190182Thread 139778838230592 finished haplotype 90
2025-12-19 13:28:36,720 - tsinfer.inference - INFO - 1766147316.7208648Thread 139778838230592 starting haplotype 95
2025-12-19 13:28:36,722 - tsinfer.inference - INFO - 1766147316.722704Thread 139778829837888 finished haplotype 92
2025-12-19 13:28:36,723 - tsinfer.inference - INFO - 1766147316.723658Thread 139778829837888 starting haplotype 96
2025-12-19 13:28:36,740 - tsinfer.inference - INFO - 1766147316.7408538Thread 139778821445184 finished haplotype 93
2025-12-19 13:28:36,741 - tsinfer.inference - INFO - 1766147316.7416692Thread 139778821445184 starting haplotype 97
2025-12-19 13:28:36,744 - tsinfer.inference - INFO - 1766147316.744034Thread 139778916025920 finished haplotype 94
2025-12-19 13:28:36,744 - tsinfer.inference - INFO - 1766147316.7447877Thread 139778916025920 starting haplotype 98
2025-12-19 13:28:36,751 - tsinfer.inference - INFO - 1766147316.7512677Thread 139778838230592 finished haplotype 95
2025-12-19 13:28:36,751 - tsinfer.inference - INFO - 1766147316.7518702Thread 139778829837888 finished haplotype 96
2025-12-19 13:28:36,753 - tsinfer.inference - INFO - 1766147316.7532423Thread 139778838230592 starting haplotype 99
2025-12-19 13:28:36,754 - tsinfer.inference - INFO - 1766147316.7547832Thread 139778829837888 starting haplotype 100
2025-12-19 13:28:36,770 - tsinfer.inference - INFO - 1766147316.770546Thread 139778821445184 finished haplotype 97
2025-12-19 13:28:36,770 - tsinfer.inference - INFO - 1766147316.7708666Thread 139778916025920 finished haplotype 98
2025-12-19 13:28:36,772 - tsinfer.inference - INFO - 1766147316.7724218Thread 139778821445184 starting haplotype 101
2025-12-19 13:28:36,774 - tsinfer.inference - INFO - 1766147316.7745862Thread 139778916025920 starting haplotype 102
2025-12-19 13:28:36,783 - tsinfer.inference - INFO - 1766147316.7834759Thread 139778838230592 finished haplotype 99
2025-12-19 13:28:36,784 - tsinfer.inference - INFO - 1766147316.7840905Thread 139778829837888 finished haplotype 100
2025-12-19 13:28:36,785 - tsinfer.inference - INFO - 1766147316.7855568Thread 139778838230592 starting haplotype 103
2025-12-19 13:28:36,787 - tsinfer.inference - INFO - 1766147316.7875042Thread 139778829837888 starting haplotype 104
2025-12-19 13:28:36,801 - tsinfer.inference - INFO - 1766147316.8014576Thread 139778821445184 finished haplotype 101
2025-12-19 13:28:36,802 - tsinfer.inference - INFO - 1766147316.8023646Thread 139778821445184 starting haplotype 105
2025-12-19 13:28:36,803 - tsinfer.inference - INFO - 1766147316.8030794Thread 139778916025920 finished haplotype 102
2025-12-19 13:28:36,804 - tsinfer.inference - INFO - 1766147316.8044784Thread 139778916025920 starting haplotype 106
2025-12-19 13:28:36,814 - tsinfer.inference - INFO - 1766147316.8147357Thread 139778838230592 finished haplotype 103
2025-12-19 13:28:36,816 - tsinfer.inference - INFO - 1766147316.8163817Thread 139778838230592 starting haplotype 107
2025-12-19 13:28:36,818 - tsinfer.inference - INFO - 1766147316.8188417Thread 139778829837888 finished haplotype 104
2025-12-19 13:28:36,820 - tsinfer.inference - INFO - 1766147316.8205936Thread 139778829837888 starting haplotype 108
2025-12-19 13:28:36,828 - tsinfer.inference - INFO - 1766147316.8288822Thread 139778821445184 finished haplotype 105
2025-12-19 13:28:36,829 - tsinfer.inference - INFO - 1766147316.8297863Thread 139778821445184 starting haplotype 109
2025-12-19 13:28:36,831 - tsinfer.inference - INFO - 1766147316.8310344Thread 139778916025920 finished haplotype 106
2025-12-19 13:28:36,831 - tsinfer.inference - INFO - 1766147316.8318424Thread 139778916025920 starting haplotype 110
2025-12-19 13:28:36,845 - tsinfer.inference - INFO - 1766147316.8455565Thread 139778838230592 finished haplotype 107
2025-12-19 13:28:36,846 - tsinfer.inference - INFO - 1766147316.8465245Thread 139778838230592 starting haplotype 111
2025-12-19 13:28:36,851 - tsinfer.inference - INFO - 1766147316.851423Thread 139778829837888 finished haplotype 108
2025-12-19 13:28:36,852 - tsinfer.inference - INFO - 1766147316.8523257Thread 139778829837888 starting haplotype 112
2025-12-19 13:28:36,856 - tsinfer.inference - INFO - 1766147316.8562217Thread 139778821445184 finished haplotype 109
2025-12-19 13:28:36,857 - tsinfer.inference - INFO - 1766147316.8570461Thread 139778821445184 starting haplotype 113
2025-12-19 13:28:36,873 - tsinfer.inference - INFO - 1766147316.8732285Thread 139778916025920 finished haplotype 110
2025-12-19 13:28:36,874 - tsinfer.inference - INFO - 1766147316.8740551Thread 139778916025920 starting haplotype 114
2025-12-19 13:28:36,886 - tsinfer.inference - INFO - 1766147316.8866622Thread 139778829837888 finished haplotype 112
2025-12-19 13:28:36,887 - tsinfer.inference - INFO - 1766147316.8874981Thread 139778829837888 starting haplotype 115
2025-12-19 13:28:36,890 - tsinfer.inference - INFO - 1766147316.8905504Thread 139778838230592 finished haplotype 111
2025-12-19 13:28:36,892 - tsinfer.inference - INFO - 1766147316.8921056Thread 139778838230592 starting haplotype 116
2025-12-19 13:28:36,894 - tsinfer.inference - INFO - 1766147316.8941097Thread 139778821445184 finished haplotype 113
2025-12-19 13:28:36,895 - tsinfer.inference - INFO - 1766147316.8958492Thread 139778821445184 starting haplotype 117
2025-12-19 13:28:36,912 - tsinfer.inference - INFO - 1766147316.9125092Thread 139778916025920 finished haplotype 114
2025-12-19 13:28:36,914 - tsinfer.inference - INFO - 1766147316.9140031Thread 139778916025920 starting haplotype 118
2025-12-19 13:28:36,922 - tsinfer.inference - INFO - 1766147316.922719Thread 139778829837888 finished haplotype 115
2025-12-19 13:28:36,924 - tsinfer.inference - INFO - 1766147316.9241867Thread 139778829837888 starting haplotype 119
2025-12-19 13:28:36,927 - tsinfer.inference - INFO - 1766147316.9277635Thread 139778838230592 finished haplotype 116
2025-12-19 13:28:36,929 - tsinfer.inference - INFO - 1766147316.92943Thread 139778838230592 starting haplotype 120
2025-12-19 13:28:36,935 - tsinfer.inference - INFO - 1766147316.9353206Thread 139778821445184 finished haplotype 117
2025-12-19 13:28:36,937 - tsinfer.inference - INFO - 1766147316.936984Thread 139778821445184 starting haplotype 121
2025-12-19 13:28:36,948 - tsinfer.inference - INFO - 1766147316.9483862Thread 139778916025920 finished haplotype 118
2025-12-19 13:28:36,950 - tsinfer.inference - INFO - 1766147316.9500341Thread 139778916025920 starting haplotype 122
2025-12-19 13:28:36,960 - tsinfer.inference - INFO - 1766147316.9602776Thread 139778829837888 finished haplotype 119
2025-12-19 13:28:36,961 - tsinfer.inference - INFO - 1766147316.961732Thread 139778829837888 starting haplotype 123
2025-12-19 13:28:36,967 - tsinfer.inference - INFO - 1766147316.967151Thread 139778838230592 finished haplotype 120
2025-12-19 13:28:36,968 - tsinfer.inference - INFO - 1766147316.9687874Thread 139778838230592 starting haplotype 124
2025-12-19 13:28:36,972 - tsinfer.inference - INFO - 1766147316.9719982Thread 139778821445184 finished haplotype 121
2025-12-19 13:28:36,972 - tsinfer.inference - INFO - 1766147316.9728394Thread 139778821445184 starting haplotype 125
2025-12-19 13:28:36,984 - tsinfer.inference - INFO - 1766147316.9847605Thread 139778916025920 finished haplotype 122
2025-12-19 13:28:36,985 - tsinfer.inference - INFO - 1766147316.9855723Thread 139778916025920 starting haplotype 126
2025-12-19 13:28:36,998 - tsinfer.inference - INFO - 1766147316.998573Thread 139778829837888 finished haplotype 123
2025-12-19 13:28:36,999 - tsinfer.inference - INFO - 1766147316.999381Thread 139778829837888 starting haplotype 127
2025-12-19 13:28:37,007 - tsinfer.inference - INFO - 1766147317.0070739Thread 139778838230592 finished haplotype 124
2025-12-19 13:28:37,008 - tsinfer.inference - INFO - 1766147317.0086203Thread 139778838230592 starting haplotype 128
2025-12-19 13:28:37,010 - tsinfer.inference - INFO - 1766147317.0109377Thread 139778821445184 finished haplotype 125
2025-12-19 13:28:37,013 - tsinfer.inference - INFO - 1766147317.013976Thread 139778821445184 starting haplotype 129
2025-12-19 13:28:37,021 - tsinfer.inference - INFO - 1766147317.021044Thread 139778916025920 finished haplotype 126
2025-12-19 13:28:37,022 - tsinfer.inference - INFO - 1766147317.0225132Thread 139778916025920 starting haplotype 130
2025-12-19 13:28:37,038 - tsinfer.inference - INFO - 1766147317.0384517Thread 139778829837888 finished haplotype 127
2025-12-19 13:28:37,039 - tsinfer.inference - INFO - 1766147317.039895Thread 139778829837888 starting haplotype 131
2025-12-19 13:28:37,049 - tsinfer.inference - INFO - 1766147317.0495496Thread 139778838230592 finished haplotype 128
2025-12-19 13:28:37,051 - tsinfer.inference - INFO - 1766147317.0512116Thread 139778838230592 starting haplotype 132
2025-12-19 13:28:37,055 - tsinfer.inference - INFO - 1766147317.0558782Thread 139778821445184 finished haplotype 129
2025-12-19 13:28:37,057 - tsinfer.inference - INFO - 1766147317.0575783Thread 139778821445184 starting haplotype 133
2025-12-19 13:28:37,061 - tsinfer.inference - INFO - 1766147317.061572Thread 139778916025920 finished haplotype 130
2025-12-19 13:28:37,063 - tsinfer.inference - INFO - 1766147317.0630276Thread 139778916025920 starting haplotype 134
2025-12-19 13:28:37,076 - tsinfer.inference - INFO - 1766147317.076113Thread 139778829837888 finished haplotype 131
2025-12-19 13:28:37,077 - tsinfer.inference - INFO - 1766147317.0775888Thread 139778829837888 starting haplotype 135
2025-12-19 13:28:37,086 - tsinfer.inference - INFO - 1766147317.0862548Thread 139778838230592 finished haplotype 132
2025-12-19 13:28:37,088 - tsinfer.inference - INFO - 1766147317.0881584Thread 139778838230592 starting haplotype 136
2025-12-19 13:28:37,096 - tsinfer.inference - INFO - 1766147317.096675Thread 139778821445184 finished haplotype 133
2025-12-19 13:28:37,098 - tsinfer.inference - INFO - 1766147317.0983086Thread 139778821445184 starting haplotype 137
2025-12-19 13:28:37,104 - tsinfer.inference - INFO - 1766147317.1044586Thread 139778916025920 finished haplotype 134
2025-12-19 13:28:37,105 - tsinfer.inference - INFO - 1766147317.105898Thread 139778916025920 starting haplotype 138
2025-12-19 13:28:37,113 - tsinfer.inference - INFO - 1766147317.1137245Thread 139778829837888 finished haplotype 135
2025-12-19 13:28:37,115 - tsinfer.inference - INFO - 1766147317.115196Thread 139778829837888 starting haplotype 139
2025-12-19 13:28:37,126 - tsinfer.inference - INFO - 1766147317.1266735Thread 139778838230592 finished haplotype 136
2025-12-19 13:28:37,130 - tsinfer.inference - INFO - 1766147317.1303258Thread 139778838230592 starting haplotype 140
2025-12-19 13:28:37,138 - tsinfer.inference - INFO - 1766147317.1387627Thread 139778821445184 finished haplotype 137
2025-12-19 13:28:37,140 - tsinfer.inference - INFO - 1766147317.1404324Thread 139778821445184 starting haplotype 141
2025-12-19 13:28:37,147 - tsinfer.inference - INFO - 1766147317.147748Thread 139778916025920 finished haplotype 138
2025-12-19 13:28:37,148 - tsinfer.inference - INFO - 1766147317.1485753Thread 139778916025920 starting haplotype 142
2025-12-19 13:28:37,161 - tsinfer.inference - INFO - 1766147317.1617641Thread 139778829837888 finished haplotype 139
2025-12-19 13:28:37,163 - tsinfer.inference - INFO - 1766147317.1632442Thread 139778829837888 starting haplotype 143
2025-12-19 13:28:37,169 - tsinfer.inference - INFO - 1766147317.169503Thread 139778838230592 finished haplotype 140
2025-12-19 13:28:37,171 - tsinfer.inference - INFO - 1766147317.1711798Thread 139778838230592 starting haplotype 144
2025-12-19 13:28:37,179 - tsinfer.inference - INFO - 1766147317.1799157Thread 139778821445184 finished haplotype 141
2025-12-19 13:28:37,181 - tsinfer.inference - INFO - 1766147317.1816044Thread 139778821445184 starting haplotype 145
2025-12-19 13:28:37,187 - tsinfer.inference - INFO - 1766147317.1878886Thread 139778916025920 finished haplotype 142
2025-12-19 13:28:37,189 - tsinfer.inference - INFO - 1766147317.1893594Thread 139778916025920 starting haplotype 146
2025-12-19 13:28:37,200 - tsinfer.inference - INFO - 1766147317.2008407Thread 139778829837888 finished haplotype 143
2025-12-19 13:28:37,202 - tsinfer.inference - INFO - 1766147317.2023127Thread 139778829837888 starting haplotype 147
2025-12-19 13:28:37,210 - tsinfer.inference - INFO - 1766147317.2109094Thread 139778838230592 finished haplotype 144
2025-12-19 13:28:37,212 - tsinfer.inference - INFO - 1766147317.2125635Thread 139778838230592 starting haplotype 148
2025-12-19 13:28:37,221 - tsinfer.inference - INFO - 1766147317.2211118Thread 139778821445184 finished haplotype 145
2025-12-19 13:28:37,222 - tsinfer.inference - INFO - 1766147317.2226608Thread 139778821445184 starting haplotype 149
2025-12-19 13:28:37,227 - tsinfer.inference - INFO - 1766147317.227511Thread 139778916025920 finished haplotype 146
2025-12-19 13:28:37,228 - tsinfer.inference - INFO - 1766147317.2289805Thread 139778916025920 starting haplotype 150
2025-12-19 13:28:37,241 - tsinfer.inference - INFO - 1766147317.2410357Thread 139778829837888 finished haplotype 147
2025-12-19 13:28:37,241 - tsinfer.inference - INFO - 1766147317.2418559Thread 139778829837888 starting haplotype 151
2025-12-19 13:28:37,253 - tsinfer.inference - INFO - 1766147317.2536976Thread 139778838230592 finished haplotype 148
2025-12-19 13:28:37,255 - tsinfer.inference - INFO - 1766147317.2553647Thread 139778838230592 starting haplotype 152
2025-12-19 13:28:37,262 - tsinfer.inference - INFO - 1766147317.2620595Thread 139778821445184 finished haplotype 149
2025-12-19 13:28:37,263 - tsinfer.inference - INFO - 1766147317.2637484Thread 139778821445184 starting haplotype 153
2025-12-19 13:28:37,265 - tsinfer.inference - INFO - 1766147317.2657816Thread 139778916025920 finished haplotype 150
2025-12-19 13:28:37,267 - tsinfer.inference - INFO - 1766147317.2672627Thread 139778916025920 starting haplotype 154
2025-12-19 13:28:37,280 - tsinfer.inference - INFO - 1766147317.2802243Thread 139778829837888 finished haplotype 151
2025-12-19 13:28:37,281 - tsinfer.inference - INFO - 1766147317.2816865Thread 139778829837888 starting haplotype 155
2025-12-19 13:28:37,293 - tsinfer.inference - INFO - 1766147317.2938395Thread 139778838230592 finished haplotype 152
2025-12-19 13:28:37,295 - tsinfer.inference - INFO - 1766147317.2954962Thread 139778838230592 starting haplotype 156
2025-12-19 13:28:37,299 - tsinfer.inference - INFO - 1766147317.2995608Thread 139778821445184 finished haplotype 153
2025-12-19 13:28:37,301 - tsinfer.inference - INFO - 1766147317.3012452Thread 139778821445184 starting haplotype 157
2025-12-19 13:28:37,309 - tsinfer.inference - INFO - 1766147317.3095279Thread 139778916025920 finished haplotype 154
2025-12-19 13:28:37,311 - tsinfer.inference - INFO - 1766147317.3111064Thread 139778916025920 starting haplotype 158
2025-12-19 13:28:37,319 - tsinfer.inference - INFO - 1766147317.319693Thread 139778829837888 finished haplotype 155
2025-12-19 13:28:37,321 - tsinfer.inference - INFO - 1766147317.3211486Thread 139778829837888 starting haplotype 159
2025-12-19 13:28:37,335 - tsinfer.inference - INFO - 1766147317.3357942Thread 139778838230592 finished haplotype 156
2025-12-19 13:28:37,336 - tsinfer.inference - INFO - 1766147317.3360171Thread 139778821445184 finished haplotype 157
2025-12-19 13:28:37,336 - tsinfer.inference - INFO - 1766147317.3369157Thread 139778838230592 starting haplotype 160
2025-12-19 13:28:37,338 - tsinfer.inference - INFO - 1766147317.338357Thread 139778821445184 starting haplotype 161
2025-12-19 13:28:37,350 - tsinfer.inference - INFO - 1766147317.350501Thread 139778916025920 finished haplotype 158
2025-12-19 13:28:37,351 - tsinfer.inference - INFO - 1766147317.3513222Thread 139778916025920 starting haplotype 162
2025-12-19 13:28:37,361 - tsinfer.inference - INFO - 1766147317.361895Thread 139778829837888 finished haplotype 159
2025-12-19 13:28:37,363 - tsinfer.inference - INFO - 1766147317.363371Thread 139778829837888 starting haplotype 163
2025-12-19 13:28:37,372 - tsinfer.inference - INFO - 1766147317.3725228Thread 139778838230592 finished haplotype 160
2025-12-19 13:28:37,373 - tsinfer.inference - INFO - 1766147317.3738105Thread 139778821445184 finished haplotype 161
2025-12-19 13:28:37,374 - tsinfer.inference - INFO - 1766147317.374202Thread 139778838230592 starting haplotype 164
2025-12-19 13:28:37,376 - tsinfer.inference - INFO - 1766147317.3763673Thread 139778821445184 starting haplotype 165
2025-12-19 13:28:37,389 - tsinfer.inference - INFO - 1766147317.3896666Thread 139778916025920 finished haplotype 162
2025-12-19 13:28:37,391 - tsinfer.inference - INFO - 1766147317.391168Thread 139778916025920 starting haplotype 166
2025-12-19 13:28:37,402 - tsinfer.inference - INFO - 1766147317.4027078Thread 139778829837888 finished haplotype 163
2025-12-19 13:28:37,404 - tsinfer.inference - INFO - 1766147317.404375Thread 139778829837888 starting haplotype 167
2025-12-19 13:28:37,415 - tsinfer.inference - INFO - 1766147317.4152668Thread 139778821445184 finished haplotype 165
2025-12-19 13:28:37,416 - tsinfer.inference - INFO - 1766147317.4160347Thread 139778838230592 finished haplotype 164
2025-12-19 13:28:37,418 - tsinfer.inference - INFO - 1766147317.418079Thread 139778838230592 starting haplotype 169
2025-12-19 13:28:37,416 - tsinfer.inference - INFO - 1766147317.416727Thread 139778821445184 starting haplotype 168
2025-12-19 13:28:37,425 - tsinfer.inference - INFO - 1766147317.4259524Thread 139778916025920 finished haplotype 166
2025-12-19 13:28:37,426 - tsinfer.inference - INFO - 1766147317.426869Thread 139778916025920 starting haplotype 170
2025-12-19 13:28:37,443 - tsinfer.inference - INFO - 1766147317.4435985Thread 139778829837888 finished haplotype 167
2025-12-19 13:28:37,444 - tsinfer.inference - INFO - 1766147317.4444156Thread 139778829837888 starting haplotype 171
2025-12-19 13:28:37,459 - tsinfer.inference - INFO - 1766147317.4591887Thread 139778821445184 finished haplotype 168
2025-12-19 13:28:37,460 - tsinfer.inference - INFO - 1766147317.460164Thread 139778838230592 finished haplotype 169
2025-12-19 13:28:37,462 - tsinfer.inference - INFO - 1766147317.4622233Thread 139778838230592 starting haplotype 173
2025-12-19 13:28:37,463 - tsinfer.inference - INFO - 1766147317.4634736Thread 139778916025920 finished haplotype 170
2025-12-19 13:28:37,464 - tsinfer.inference - INFO - 1766147317.4645045Thread 139778916025920 starting haplotype 174
2025-12-19 13:28:37,460 - tsinfer.inference - INFO - 1766147317.460692Thread 139778821445184 starting haplotype 172
2025-12-19 13:28:37,482 - tsinfer.inference - INFO - 1766147317.4826436Thread 139778829837888 finished haplotype 171
2025-12-19 13:28:37,484 - tsinfer.inference - INFO - 1766147317.4840982Thread 139778829837888 starting haplotype 175
2025-12-19 13:28:37,497 - tsinfer.inference - INFO - 1766147317.4978175Thread 139778916025920 finished haplotype 174
2025-12-19 13:28:37,499 - tsinfer.inference - INFO - 1766147317.4992702Thread 139778916025920 starting haplotype 176
2025-12-19 13:28:37,500 - tsinfer.inference - INFO - 1766147317.500409Thread 139778838230592 finished haplotype 173
2025-12-19 13:28:37,502 - tsinfer.inference - INFO - 1766147317.5029466Thread 139778838230592 starting haplotype 177
2025-12-19 13:28:37,504 - tsinfer.inference - INFO - 1766147317.5041585Thread 139778821445184 finished haplotype 172
2025-12-19 13:28:37,506 - tsinfer.inference - INFO - 1766147317.506543Thread 139778821445184 starting haplotype 178
2025-12-19 13:28:37,526 - tsinfer.inference - INFO - 1766147317.526261Thread 139778829837888 finished haplotype 175
2025-12-19 13:28:37,527 - tsinfer.inference - INFO - 1766147317.5277095Thread 139778829837888 starting haplotype 179
2025-12-19 13:28:37,534 - tsinfer.inference - INFO - 1766147317.5343258Thread 139778916025920 finished haplotype 176
2025-12-19 13:28:37,535 - tsinfer.inference - INFO - 1766147317.5357652Thread 139778916025920 starting haplotype 180
2025-12-19 13:28:37,541 - tsinfer.inference - INFO - 1766147317.5410419Thread 139778838230592 finished haplotype 177
2025-12-19 13:28:37,542 - tsinfer.inference - INFO - 1766147317.542693Thread 139778838230592 starting haplotype 181
2025-12-19 13:28:37,544 - tsinfer.inference - INFO - 1766147317.5445113Thread 139778821445184 finished haplotype 178
2025-12-19 13:28:37,546 - tsinfer.inference - INFO - 1766147317.5461051Thread 139778821445184 starting haplotype 182
2025-12-19 13:28:37,566 - tsinfer.inference - INFO - 1766147317.5666895Thread 139778829837888 finished haplotype 179
2025-12-19 13:28:37,568 - tsinfer.inference - INFO - 1766147317.5681353Thread 139778829837888 starting haplotype 183
2025-12-19 13:28:37,574 - tsinfer.inference - INFO - 1766147317.5743012Thread 139778916025920 finished haplotype 180
2025-12-19 13:28:37,575 - tsinfer.inference - INFO - 1766147317.5757627Thread 139778916025920 starting haplotype 184
2025-12-19 13:28:37,584 - tsinfer.inference - INFO - 1766147317.5845551Thread 139778838230592 finished haplotype 181
2025-12-19 13:28:37,585 - tsinfer.inference - INFO - 1766147317.5853362Thread 139778821445184 finished haplotype 182
2025-12-19 13:28:37,586 - tsinfer.inference - INFO - 1766147317.586257Thread 139778838230592 starting haplotype 185
2025-12-19 13:28:37,588 - tsinfer.inference - INFO - 1766147317.5885925Thread 139778821445184 starting haplotype 186
2025-12-19 13:28:37,605 - tsinfer.inference - INFO - 1766147317.6056733Thread 139778829837888 finished haplotype 183
2025-12-19 13:28:37,606 - tsinfer.inference - INFO - 1766147317.60651Thread 139778829837888 starting haplotype 187
2025-12-19 13:28:37,615 - tsinfer.inference - INFO - 1766147317.615969Thread 139778916025920 finished haplotype 184
2025-12-19 13:28:37,616 - tsinfer.inference - INFO - 1766147317.616799Thread 139778916025920 starting haplotype 188
2025-12-19 13:28:37,624 - tsinfer.inference - INFO - 1766147317.6245868Thread 139778821445184 finished haplotype 186
2025-12-19 13:28:37,625 - tsinfer.inference - INFO - 1766147317.6253898Thread 139778821445184 starting haplotype 189
2025-12-19 13:28:37,631 - tsinfer.inference - INFO - 1766147317.631196Thread 139778838230592 finished haplotype 185
2025-12-19 13:28:37,632 - tsinfer.inference - INFO - 1766147317.6327467Thread 139778838230592 starting haplotype 190
2025-12-19 13:28:37,647 - tsinfer.inference - INFO - 1766147317.647945Thread 139778829837888 finished haplotype 187
2025-12-19 13:28:37,648 - tsinfer.inference - INFO - 1766147317.6488066Thread 139778829837888 starting haplotype 191
2025-12-19 13:28:37,654 - tsinfer.inference - INFO - 1766147317.65467Thread 139778916025920 finished haplotype 188
2025-12-19 13:28:37,655 - tsinfer.inference - INFO - 1766147317.6554816Thread 139778916025920 starting haplotype 192
2025-12-19 13:28:37,666 - tsinfer.inference - INFO - 1766147317.6669776Thread 139778821445184 finished haplotype 189
2025-12-19 13:28:37,667 - tsinfer.inference - INFO - 1766147317.6677787Thread 139778821445184 starting haplotype 193
2025-12-19 13:28:37,676 - tsinfer.inference - INFO - 1766147317.6763363Thread 139778838230592 finished haplotype 190
2025-12-19 13:28:37,677 - tsinfer.inference - INFO - 1766147317.6778665Thread 139778838230592 starting haplotype 194
2025-12-19 13:28:37,685 - tsinfer.inference - INFO - 1766147317.6852717Thread 139778829837888 finished haplotype 191
2025-12-19 13:28:37,687 - tsinfer.inference - INFO - 1766147317.6870525Thread 139778829837888 starting haplotype 195
2025-12-19 13:28:37,693 - tsinfer.inference - INFO - 1766147317.69394Thread 139778916025920 finished haplotype 192
2025-12-19 13:28:37,695 - tsinfer.inference - INFO - 1766147317.6953895Thread 139778916025920 starting haplotype 196
2025-12-19 13:28:37,705 - tsinfer.inference - INFO - 1766147317.7052002Thread 139778821445184 finished haplotype 193
2025-12-19 13:28:37,706 - tsinfer.inference - INFO - 1766147317.7066617Thread 139778821445184 starting haplotype 197
2025-12-19 13:28:37,715 - tsinfer.inference - INFO - 1766147317.7155938Thread 139778838230592 finished haplotype 194
2025-12-19 13:28:37,717 - tsinfer.inference - INFO - 1766147317.7172399Thread 139778838230592 starting haplotype 198
2025-12-19 13:28:37,728 - tsinfer.inference - INFO - 1766147317.7287219Thread 139778829837888 finished haplotype 195
2025-12-19 13:28:37,730 - tsinfer.inference - INFO - 1766147317.7302806Thread 139778829837888 starting haplotype 199
2025-12-19 13:28:37,737 - tsinfer.inference - INFO - 1766147317.737464Thread 139778916025920 finished haplotype 196
2025-12-19 13:28:37,738 - tsinfer.inference - INFO - 1766147317.7389247Thread 139778916025920 starting haplotype 200
2025-12-19 13:28:37,744 - tsinfer.inference - INFO - 1766147317.7446089Thread 139778821445184 finished haplotype 197
2025-12-19 13:28:37,746 - tsinfer.inference - INFO - 1766147317.7460592Thread 139778821445184 starting haplotype 201
2025-12-19 13:28:37,755 - tsinfer.inference - INFO - 1766147317.7554412Thread 139778838230592 finished haplotype 198
2025-12-19 13:28:37,756 - tsinfer.inference - INFO - 1766147317.7563453Thread 139778838230592 starting haplotype 202
2025-12-19 13:28:37,764 - tsinfer.inference - INFO - 1766147317.7649527Thread 139778829837888 finished haplotype 199
2025-12-19 13:28:37,765 - tsinfer.inference - INFO - 1766147317.7658935Thread 139778829837888 starting haplotype 203
2025-12-19 13:28:37,782 - tsinfer.inference - INFO - 1766147317.7823172Thread 139778916025920 finished haplotype 200
2025-12-19 13:28:37,783 - tsinfer.inference - INFO - 1766147317.783135Thread 139778916025920 starting haplotype 204
2025-12-19 13:28:37,789 - tsinfer.inference - INFO - 1766147317.788986Thread 139778821445184 finished haplotype 201
2025-12-19 13:28:37,790 - tsinfer.inference - INFO - 1766147317.7904818Thread 139778821445184 starting haplotype 205
2025-12-19 13:28:37,790 - tsinfer.inference - INFO - 1766147317.7907784Thread 139778838230592 finished haplotype 202
2025-12-19 13:28:37,792 - tsinfer.inference - INFO - 1766147317.7927718Thread 139778838230592 starting haplotype 206
2025-12-19 13:28:37,801 - tsinfer.inference - INFO - 1766147317.8019044Thread 139778829837888 finished haplotype 203
2025-12-19 13:28:37,802 - tsinfer.inference - INFO - 1766147317.802853Thread 139778829837888 starting haplotype 207
2025-12-19 13:28:37,817 - tsinfer.inference - INFO - 1766147317.8175802Thread 139778916025920 finished haplotype 204
2025-12-19 13:28:37,818 - tsinfer.inference - INFO - 1766147317.8184059Thread 139778916025920 starting haplotype 208
2025-12-19 13:28:37,827 - tsinfer.inference - INFO - 1766147317.8277097Thread 139778838230592 finished haplotype 206
2025-12-19 13:28:37,828 - tsinfer.inference - INFO - 1766147317.8285773Thread 139778838230592 starting haplotype 209
2025-12-19 13:28:37,831 - tsinfer.inference - INFO - 1766147317.8310258Thread 139778821445184 finished haplotype 205
2025-12-19 13:28:37,841 - tsinfer.inference - INFO - 1766147317.841623Thread 139778829837888 finished haplotype 207
2025-12-19 13:28:37,852 - tsinfer.inference - INFO - 1766147317.8519914Thread 139778916025920 finished haplotype 208
2025-12-19 13:28:37,864 - tsinfer.inference - INFO - 1766147317.8644433Thread 139778838230592 finished haplotype 209
2025-12-19 13:28:37,865 - tsinfer.inference - INFO - Finished matching for all samples in 1.86 seconds
2025-12-19 13:28:37,866 - tsinfer.inference - INFO - Inserting sample paths: 8898 edges in total
2025-12-19 13:28:37,895 - tsinfer.inference - INFO - Finalising tree sequence
2025-12-19 13:28:38,009 - tsinfer.inference - INFO - Built samples tree sequence: 7253 nodes (572 pc); 37880 edges; 8605 sites; 8605 mutations
2025-12-19 13:28:38,013 - tsinfer.inference - INFO - Mapping additional sites
2025-12-19 13:28:38,941 - tsinfer.inference - INFO - Removing the oldest edge to detach the virtual-root-like ancestor
2025-12-19 13:28:38,984 - tsinfer.inference - INFO - Located the all zeros ultimate ancestor
2025-12-19 13:28:38,996 - tsinfer.inference - INFO - Splitting ultimate ancestor into 1386 nodes
2025-12-19 13:28:39,066 - tsinfer.inference - INFO - Erased flanks covering 0.0119% of the genome: 108.0 units at the start and 11.0 units at the end
2025-12-19 13:28:39,067 - tsinfer.inference - INFO - Simplifying with filter_sites=False, filter_populations=False, filter_individuals=False, and keep_unary=True on 8639 nodes and 41530 edges
2025-12-19 13:28:39,080 - tsinfer.inference - INFO - Finished simplify; now have 8550 nodes and 31651 edges
Inferred tree sequence `ts`: 5708 trees over 1.0 Mb
ts
Tree Sequence
|
|
|---|---|
| Trees | 5 708 |
| Sequence Length | 1 000 000 |
| Time Units | uncalibrated |
| Sample Nodes | 210 |
| Total Size | 3.1 MiB |
| Metadata |
dict |
| Table | Rows | Size | Has Metadata |
|---|---|---|---|
| Edges | 41 316 | 1.3 MiB | |
| Individuals | 105 | 4.7 KiB | ✅ |
| Migrations | 0 | 8 Bytes | |
| Mutations | 12 844 | 464.1 KiB | |
| Nodes | 7 651 | 384.5 KiB | ✅ |
| Populations | 3 | 88 Bytes | ✅ |
| Provenances | 2 | 1.2 KiB | |
| Sites | 12 844 | 660.4 KiB | ✅ |
| Provenance Timestamp | Software Name | Version | Command | Full record |
|---|---|---|---|---|
| 19 December, 2025 at 01:28:39 PM | tskit | 1.0.0b3 | simplify |
Detailsdictschema_version: 1.0.0
software:
dictname: tskitversion: 1.0.0b3
parameters:
dictcommand: simplifyTODO: add simplify parameters
environment:
dict
os:
dictsystem: Linuxnode: node1 release: 5.15.0-58-generic version: #64-Ubuntu SMP Thu Jan 5 11:43:13 UTC 2023 machine: x86_64
python:
dictimplementation: CPythonversion: 3.12.12
libraries:
dict
kastore:
dictversion: 2.1.1 |
| 19 December, 2025 at 01:28:39 PM | tsinfer | 0.5.0 | infer |
Detailsdictschema_version: 1.0.0
software:
dictname: tsinferversion: 0.5.0
parameters:
dictmismatch_ratio: Nonepath_compression: True precision: None post_process: None command: infer
environment:
dict
libraries:
dict
zarr:
dictversion: 2.18.7
numcodecs:
dictversion: 0.15.0
lmdb:
dictversion: 1.7.5
tskit:
dictversion: 1.0.0b3
os:
dictsystem: Linuxnode: node1 release: 5.15.0-58-generic version: #64-Ubuntu SMP Thu Jan 5 11:43:13 UTC 2023 machine: x86_64
python:
dictimplementation: CPython
version:
list312 12
resources:
dictelapsed_time: 17.824354261159897user_time: 39.0 sys_time: 1.2200000000000002 max_memory: 849477632 |
To cite this software, please consult the citation manual: https://tskit.dev/citation/
# Removes unary nodes (currently required in tsdate), keeps historical-only sites
ts = tsdate.preprocess_ts(ts, filter_sites=False)
ts = tsdate.date(
ts,
method="inside_outside",
mutation_rate=1e-8,
Ne=1e4
)
ts
2025-12-19 13:28:39,154 - tsdate.util - INFO - Beginning preprocessing
2025-12-19 13:28:39,155 - tsdate.util - INFO - Minimum_gap: None and erase_flanks: None
2025-12-19 13:28:39,156 - tsdate.util - INFO - REMOVING TELOMERE: Snip topology from 0 to first site at 107.0.
2025-12-19 13:28:39,157 - tsdate.util - INFO - REMOVING TELOMERE: Snip topology from 999989.0 to end of sequence at 1000000.0.
2025-12-19 13:28:59,396 - tsdate.core - INFO - Inserted node and mutation metadata in 0.2915797233581543 seconds
2025-12-19 13:28:59,398 - root - INFO - Modified ages of 1860 nodes to satisfy constraints
2025-12-19 13:28:59,399 - tsdate.core - INFO - Constrained node ages in 0.00 seconds
2025-12-19 13:28:59,429 - root - INFO - Set ages of 0 nonsegregating mutations to root times.
|
Tree Sequence
|
|
|---|---|
| Trees | 5 708 |
| Sequence Length | 1 000 000 |
| Time Units | generations |
| Sample Nodes | 210 |
| Total Size | 3.6 MiB |
| Metadata |
dict |
| Table | Rows | Size | Has Metadata |
|---|---|---|---|
| Edges | 41 316 | 1.3 MiB | |
| Individuals | 105 | 4.7 KiB | ✅ |
| Migrations | 0 | 8 Bytes | |
| Mutations | 12 844 | 464.1 KiB | |
| Nodes | 9 767 | 983.7 KiB | ✅ |
| Populations | 3 | 88 Bytes | ✅ |
| Provenances | 4 | 2.8 KiB | |
| Sites | 12 844 | 660.4 KiB | ✅ |
| Provenance Timestamp | Software Name | Version | Command | Full record |
|---|---|---|---|---|
| 19 December, 2025 at 01:28:59 PM | tsdate | 0.2.4 | inside_outside |
Detailsdictschema_version: 1.0.0
software:
dictname: tsdateversion: 0.2.4
parameters:
dictmutation_rate: 1e-08recombination_rate: None time_units: None progress: None population_size: 10000.0 eps: 1e-10 outside_standardize: True ignore_oldest_root: False probability_space: logarithmic num_threads: None cache_inside: False command: inside_outside
environment:
dict
os:
dictsystem: Linuxnode: node1 release: 5.15.0-58-generic version: #64-Ubuntu SMP Thu Jan 5 11:43:13 UTC 2023 machine: x86_64
python:
dictimplementation: CPythonversion: 3.12.12
libraries:
dict
tskit:
dictversion: 1.0.0b3
resources:
dictelapsed_time: 20.131826400756836user_time: 124.33 sys_time: 4.99 max_memory: 1109147648 |
| 19 December, 2025 at 01:28:39 PM | tsdate | 0.2.4 | preprocess_ts |
Detailsdictschema_version: 1.0.0
software:
dictname: tsdateversion: 0.2.4
parameters:
dictminimum_gap: 1000000erase_flanks: True split_disjoint: True filter_populations: False filter_individuals: False filter_sites: False
delete_intervals:
listlist0107.0 list999989.01000000.0 command: preprocess_ts
environment:
dict
os:
dictsystem: Linuxnode: node1 release: 5.15.0-58-generic version: #64-Ubuntu SMP Thu Jan 5 11:43:13 UTC 2023 machine: x86_64
python:
dictimplementation: CPythonversion: 3.12.12
libraries:
dict
tskit:
dictversion: 1.0.0b3
resources:
dictelapsed_time: 0.13898420333862305user_time: 104.69 sys_time: 4.53 max_memory: 849477632 |
| 19 December, 2025 at 01:28:39 PM | tskit | 1.0.0b3 | simplify |
Detailsdictschema_version: 1.0.0
software:
dictname: tskitversion: 1.0.0b3
parameters:
dictcommand: simplifyTODO: add simplify parameters
environment:
dict
os:
dictsystem: Linuxnode: node1 release: 5.15.0-58-generic version: #64-Ubuntu SMP Thu Jan 5 11:43:13 UTC 2023 machine: x86_64
python:
dictimplementation: CPythonversion: 3.12.12
libraries:
dict
kastore:
dictversion: 2.1.1 |
| 19 December, 2025 at 01:28:39 PM | tsinfer | 0.5.0 | infer |
Detailsdictschema_version: 1.0.0
software:
dictname: tsinferversion: 0.5.0
parameters:
dictmismatch_ratio: Nonepath_compression: True precision: None post_process: None command: infer
environment:
dict
libraries:
dict
zarr:
dictversion: 2.18.7
numcodecs:
dictversion: 0.15.0
lmdb:
dictversion: 1.7.5
tskit:
dictversion: 1.0.0b3
os:
dictsystem: Linuxnode: node1 release: 5.15.0-58-generic version: #64-Ubuntu SMP Thu Jan 5 11:43:13 UTC 2023 machine: x86_64
python:
dictimplementation: CPython
version:
list312 12
resources:
dictelapsed_time: 17.824354261159897user_time: 39.0 sys_time: 1.2200000000000002 max_memory: 849477632 |
To cite this software, please consult the citation manual: https://tskit.dev/citation/
dump the treesequence file:
# save generated tree
ts.dump(get_project_dir() / "tests/test1M.out.inf.trees")
I want to try to collect the first tree like I did in a previous example:
POS = 108
tree = ts.at(POS)
tree
|
Tree
|
|
|---|---|
| Index | 1 |
| Interval | 108-372 (264) |
| Roots | 1 |
| Nodes | 317 |
| Sites | 4 |
| Mutations | 4 |
| Total Branch Length | 589 912.76 |
Now get the intervals of this tree. Then try to filter out edges between those positions:
interval = tree.interval
left_bound = interval.left
right_bound = interval.right
filtered_edges = ts.tables.edges[
np.logical_and(ts.tables.edges.left >= left_bound, ts.tables.edges.right <= right_bound)]
filtered_edges[:10]
| id | left | right | parent | child | metadata |
|---|---|---|---|---|---|
| 0 | 108 | 372 | 4,415 | 2,559 |
len(filtered_edges)
1
why so few edges in this cases? How I can draw a tree with so few edges? Maybe the table itself doesn’t model every connection between nodes. Or the way I collect data on edges is completely wrong.
Can I filter out the nodes in the same way? In this case I don’t have a left and right position like in the edge table. However, from the edge table I can derive which nodes are child of parents:
parents = set(filtered_edges.parent)
childs = set(filtered_edges.child)
node_ids = parents.union(childs)
print(f"Got {len(node_ids)} distinct nodes")
Got 2 distinct nodes
# heavy intensive operation
# tree.draw_svg(
# size=(800, 400),
# time_scale="log_time",
# )
Exploring nucleotide diversity#
Calculate diversity per SNP positions: use the create_windows function and select all the
odd positions:
# remove the 0 values will be enough!
ts_diversity = ts.diversity(windows=create_windows(ts))
ts_diversity = ts_diversity[ts_diversity > 0]
ts_diversity[:10]
array([0.18086124, 0.01895648, 0.00952381, 0.00952381, 0.04670768,
0.06475279, 0.06475279, 0.00952381, 0.01895648, 0.04670768])
Now let’s compare the nucleotide diversity calculated using vcftools: here’s the command line to calculate nucleotide diversity per site:
cd test
vcftools --gzvcf test1M.out.inf.vcf.gz --out allsamples_pi --site-pi
The allsamples_pi.sites.pi is a TSV file with the positions and the nucleotide diversity. Read it with pandas:
vcftools_diversity = pd.read_csv(get_project_dir() / "experiments/test1M/allsamples_pi.sites.pi", sep="\t")
vcftools_diversity.head()
| CHROM | POS | PI | |
|---|---|---|---|
| 0 | 1 | 108 | 0.180861 |
| 1 | 1 | 120 | 0.018957 |
| 2 | 1 | 307 | 0.009524 |
| 3 | 1 | 355 | 0.009524 |
| 4 | 1 | 372 | 0.046708 |
print(f"ts_diversity is {len(ts_diversity)} in size")
print(f"vcftools_diversity is {len(vcftools_diversity)} in size")
ts_diversity is 12844 in size
vcftools_diversity is 12885 in size
this dataframe has more values than ts_diversity, since there are duplicated positions. Since I’ve
dropped duplicated positions in create_windows, I need to drop duplicates in this dataframe. However
the diveristy I can misure in those points will be different:
vcftools_diversity.drop_duplicates(subset='POS', keep='first', inplace=True)
Are this values similar?
np.isclose(ts_diversity, vcftools_diversity["PI"], atol=1e-6).all()
np.True_
Calculate diversity using branch:
# remove the 0 values will be enough!
ts_diversity_branch = ts.diversity(mode='branch', windows=create_windows(ts))
ts_diversity_branch = ts_diversity_branch[ts_diversity_branch > 0]
print(ts_diversity_branch[:10])
print(f"ts_diversity_branch is {len(ts_diversity_branch)} in size")
[46964.58318809 46964.58318809 46964.58318809 46964.58318809
46964.58318809 46964.58318809 46964.58318809 46964.58318809
45812.75375712 45812.75375712]
ts_diversity_branch is 25579 in size
print(ts.diversity(mode='branch', windows=create_windows(ts))[:10])
print(create_windows(ts)[:10])
[ 0. 46964.58318809 46964.58318809 46964.58318809
46964.58318809 46964.58318809 46964.58318809 46964.58318809
46964.58318809 45812.75375712]
[ 0. 108. 109. 120. 121. 307. 308. 355. 356. 372.]
Try to plot the tow different diversities with vcftools output:
plt.scatter(ts_diversity, vcftools_diversity["PI"])
<matplotlib.collections.PathCollection at 0x7f20dda4b020>
The branch nuclueotide diversity need to be fixed: it doesn’t have 0 in positions between windows:
# plt.scatter(ts_diversity_branch, vcftools_diversity["PI"])
# plt.xlim(0, 300)