Generalization of tgp_chr20.trees rule to other chromosomes fails

[lukashuebner]

I tried extending your workflow described in the Makefile of https://github.com/awohns/unified_genealogy_paper/tree/master/all-data to the other chromosomes by generalizing your rule

tgp_chr20.trees: tgp_chr20.samples
        python3 ../src/run_inference.py $^ -t ${NUM_THREADS} -A 1 -S 1
        python3 tsutil.py simplify tgp_chr20.nosimplify.trees $@

to

tgp_chr%.trees: tgp_chr%.samples
        python3 ../src/run_inference.py $^ -t ${NUM_THREADS} -A 1 -S 1
        python3 tsutil.py simplify tgp_chr$*.nosimplify.trees $@

This seems to work (i.e., there is no error) for chromosomes 8, 13, 19, 21, and 22 but sadly not for the others. For them, I get the following error:

python3 ../src/run_inference.py tgp_chr18.samples -t 0 -A 1 -S 1
ga-add   (1/2)100%|██████████| 1.98M/1.98M [01:39, 19.9kit/s]
ga-gen   (2/2)100%|██████████| 887k/887k [45:26, 325it/s]
Using chr18 from HapMapII_GRCh37 for the recombination map
Traceback (most recent call last):
  File "../src/run_tsinfer.py", line 230, in <module>
    main()
  File "../src/run_tsinfer.py", line 206, in main
    r_prob, m_prob = get_rho(anc, genetic_map, args.prefix)
  File "../src/run_tsinfer.py", line 109, in get_rho
    genetic_dists = tsinfer.Matcher.recombination_rate_to_dist(rmap, inference_pos)
  File "/home/huebner/projects/tree-sequences/unified_genealogy_paper/venv/lib/python3.8/site-packages/tsinfer/inference.py", line 1160, in recombination_rate_to_dist
    return np.diff(rho.get_cumulative_mass(positions))
  File "/home/huebner/projects/tree-sequences/unified_genealogy_paper/venv/lib/python3.8/site-packages/msprime/intervals.py", line 253, in get_cumulative_mass
    raise ValueError(f"Cannot have positions < 0 or > {self.sequence_length}")
ValueError: Cannot have positions < 0 or > 62949445.0
Traceback (most recent call last):
  File "../src/run_tsinfer.py", line 230, in <module>
    main()
  File "../src/run_tsinfer.py", line 212, in main
    inferred_anc_ts = tskit.load(args.prefix + ".atrees")
  File "/home/huebner/projects/tree-sequences/unified_genealogy_paper/venv/lib/python3.8/site-packages/tskit/trees.py", line 3292, in load
    return TreeSequence.load(
  File "/home/huebner/projects/tree-sequences/unified_genealogy_paper/venv/lib/python3.8/site-packages/tskit/trees.py", line 4087, in load
    file, local_file = util.convert_file_like_to_open_file(file_or_path, "rb")
  File "/home/huebner/projects/tree-sequences/unified_genealogy_paper/venv/lib/python3.8/site-packages/tskit/util.py", line 692, in convert_file_like_to_open_file
    _file = open(path, mode)
FileNotFoundError: [Errno 2] No such file or directory: 'tgp_chr18.atrees'
Running inference with Params(sample_data=<tsinfer.formats.SampleData object at 0x7f57ab7198b0>, filename='tgp_chr18.samples', genetic_map='None', ma_mut_rate=1.0, ms_mut_rate=1.0, precision=15, num_threads=0)
GA done (ma_mut: 1.0, ms_mut: 1.0)
Starting 1.0 1.0 precision 15
MA done (ma_mut:1.0 ms_mut1.0)
Traceback (most recent call last):
  File "../src/run_inference.py", line 238, in <module>
    result = run(params)
  File "../src/run_inference.py", line 99, in run
    inferred_ts = tskit.load(prefix + ".nosimplify.trees")
  File "/home/huebner/projects/tree-sequences/unified_genealogy_paper/venv/lib/python3.8/site-packages/tskit/trees.py", line 3292, in load
    return TreeSequence.load(
  File "/home/huebner/projects/tree-sequences/unified_genealogy_paper/venv/lib/python3.8/site-packages/tskit/trees.py", line 4087, in load
    file, local_file = util.convert_file_like_to_open_file(file_or_path, "rb")
  File "/home/huebner/projects/tree-sequences/unified_genealogy_paper/venv/lib/python3.8/site-packages/tskit/util.py", line 692, in convert_file_like_to_open_file
    _file = open(path, mode)
FileNotFoundError: [Errno 2] No such file or directory: 'tgp_chr18.nosimplify.trees'
make: *** [Makefile:43: tgp_chr18.trees] Error 1

As it prints "Using chr18 from HapMapII_GRCh37 for the recombination map", it probably took the broken code path in

unified_genealogy_paper/src/run_tsinfer.py

Line 105 in 51dc913

map_file = os.path.join(map.map_cache_dir, map.file_pattern.format(id="20"))