Download windows/a2/Constant/samples/PLAN.json from Larrivhan/NeCast-benchmark: direct link, hf CLI and curl.
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11.7 kB
| { | |
| "schema_version": 1, | |
| "kind": "dlcoalsim_generation_plan", | |
| "sample_generation_config": { | |
| "version": 1, | |
| "generator_schema_version": 1, | |
| "algorithm": "sha256", | |
| "sha256": "55dcc7e5df747111fbab8705f94fa4959ba90ce95cf8448e2f22d5f0f273e97b", | |
| "ignored_fields": [ | |
| "compute_chunk_size", | |
| "dataset_name", | |
| "force", | |
| "out_dir", | |
| "workers" | |
| ], | |
| "config": { | |
| "preset": "full_v01", | |
| "seed": 2071955150, | |
| "demography_mixture_version": "v1", | |
| "n_samples": 12, | |
| "shard_size": 100, | |
| "seq_len": 30000000, | |
| "n_haplotypes": 128, | |
| "time_bins": 64, | |
| "demography_resolution_log10": 0.005, | |
| "min_time": 50.0, | |
| "max_time": 500000.0, | |
| "baseline_mu": 1.25e-08, | |
| "baseline_rec": 1e-08, | |
| "p_clean_constant": 1.0, | |
| "p_random_global": 0.0, | |
| "p_custom_hetero": 0.0, | |
| "p_empirical_slice": 0.0, | |
| "p_stdpopsim_anchor": 0.0, | |
| "p_constant": 0.0, | |
| "p_spectral_walk": 0.0, | |
| "p_size_event": 0.0, | |
| "p_multi_event": 0.0, | |
| "p_exponential": 0.0, | |
| "p_sawtooth": 0.0, | |
| "p_literature_sawtooth": 0.0, | |
| "p_bottleneck": 0.0, | |
| "p_event_on_background": 0.0, | |
| "p_ooa_chain": 0.0, | |
| "p_empirical_human_ne_template": 0.0, | |
| "p_stdpopsim_single_pop": 1.0, | |
| "empirical_ne_template_dir": "templates/human_ne", | |
| "stdpopsim_template_path": "$WORK/bench_h2h_20260915/scenarios/Constant/trajectories.csv", | |
| "empirical_ne_template_source_mix": "smcpp_1kg:0.25,phlash_unified:0.60,phlash_super:0.10,msmc2_example:0.04,msmc_im_example:0.01", | |
| "empirical_ne_template_log10_shift_sd": 0.7, | |
| "empirical_ne_template_contrast_sd": 0.1, | |
| "empirical_ne_template_time_warp_sd": 0.15, | |
| "empirical_ne_template_bin_noise_sd": 0.025, | |
| "map_segments_min": 128, | |
| "map_segments_max": 512, | |
| "observed_map_noise": 0.55, | |
| "empirical_map_noise": 0.8, | |
| "hotspot_missing_prob": 0.1, | |
| "recomb_map": "maps/decode2019_avg_hg38.bed", | |
| "mut_map": "maps/roulette_2023_autosomes_hg38_1000bp.bed", | |
| "recomb_map_unit": "cM_per_Mb", | |
| "mut_map_unit": "per_bp", | |
| "mut_map_scale_to_baseline": true, | |
| "false_variant_rate_per_bp_min": 1.5e-05, | |
| "false_variant_rate_per_bp_max": 0.0006, | |
| "genotype_error_min": 0.001, | |
| "genotype_error_max": 0.004, | |
| "missing_rate_min": 0.002, | |
| "missing_rate_max": 0.02, | |
| "phase_switch_rate_per_het_min": 0.002, | |
| "phase_switch_rate_per_het_max": 0.02, | |
| "enable_stdpopsim": false, | |
| "stdpopsim_species": "HomSap", | |
| "stdpopsim_models": "", | |
| "stdpopsim_contig_length": 0, | |
| "compression": true, | |
| "compression_level": 1, | |
| "arg_detail": "summary", | |
| "arg_fraction": 1.0, | |
| "include_truth": false, | |
| "truth_fraction": 0.02, | |
| "max_retries": 3 | |
| } | |
| }, | |
| "layout": { | |
| "n_samples": 12, | |
| "shard_size": 100, | |
| "compute_chunk_size": 4, | |
| "n_shards": 1, | |
| "n_chunks": 3, | |
| "sample_id_rule": "sim_{global_sample_index:08d}", | |
| "seed_rule": "config.seed + global_sample_index * 7919", | |
| "partition_rule": "chunk_idx_mod_world_size", | |
| "array_schema_version": 1 | |
| }, | |
| "layout_sha256": "0bac3e07e7249feb72b79bf5970bb946ff68c79de75e9735f2e268b0319e3ee4", | |
| "empirical_maps": { | |
| "mutation": { | |
| "chromosomes": [ | |
| "chr1", | |
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| "chr4", | |
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| "chr19", | |
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| "chr21", | |
| "chr22" | |
| ], | |
| "mean_rate_after_scaling": 7.85305528478466e-09, | |
| "mean_rate_before_scaling": 7.85305528478466e-09, | |
| "n_chromosomes": 22, | |
| "path": "$DATA/DLCoalSim/gen-deploy-20260822-tolerance-v3/simulator/assets/maps/roulette_2023_autosomes_hg38_1000bp.bed", | |
| "rate_unit_after": "per_bp_per_generation", | |
| "rate_unit_before": "per_bp", | |
| "requested_rate_unit": "per_bp", | |
| "scaling_method": "identity", | |
| "source_formats": [ | |
| "bed_intervals" | |
| ], | |
| "source_sha256": "24b05817798a81873ad5830a3fc5ec1581b994f42adbc403270a1479f7115b5f", | |
| "source_size_bytes": 101944931 | |
| }, | |
| "recombination": { | |
| "chromosomes": [ | |
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| ], | |
| "mean_rate_after_scaling": 1.60685342677233e-07, | |
| "mean_rate_before_scaling": 16.068534267723297, | |
| "n_chromosomes": 22, | |
| "path": "$DATA/DLCoalSim/gen-deploy-20260822-tolerance-v3/simulator/assets/maps/decode2019_avg_hg38.bed", | |
| "rate_unit_after": "per_bp_per_generation", | |
| "rate_unit_before": "cM_per_Mb", | |
| "requested_rate_unit": "cM_per_Mb", | |
| "scaling_method": "cM_per_Mb_to_per_bp_per_generation", | |
| "source_formats": [ | |
| "bed_intervals" | |
| ], | |
| "source_sha256": "1a61cd217c48fff272671885c06f9f8b4018e30bffbe54031ba0b82d392a3c17", | |
| "source_size_bytes": 20815651 | |
| } | |
| }, | |
| "parsed_empirical_maps": { | |
| "parsed_maps_sha256": "16a8d37d82d6b95d9a14c01249377eaed1ad5933b0e9119ae73a1cc587d8a1fd", | |
| "n_recombination_chromosomes": 22, | |
| "n_mutation_chromosomes": 22 | |
| }, | |
| "empirical_maps_sha256": "dca1217ec36385a6e0f4fd395c7223abfa32fd056274c516ac5cbc58c7678ad4", | |
| "empirical_ne_templates": { | |
| "enabled": false, | |
| "templates": { | |
| "n_templates": 0, | |
| "source_counts": {}, | |
| "parsed_templates_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", | |
| "source_files": [] | |
| } | |
| }, | |
| "empirical_ne_templates_sha256": "252198138fd36fbb3500a38f63e81f9ad09426e6c9e26746ebb2b52fe0b4f525", | |
| "runtime_environment": { | |
| "python_implementation": "CPython", | |
| "python_version": "3.11.15", | |
| "packages": { | |
| "msprime": "1.4.2", | |
| "tskit": "1.0.3", | |
| "numpy": "2.4.6", | |
| "pandas": "3.0.5", | |
| "demes": "0.2.3", | |
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| }, | |
| "generator_source_sha256": "fc79da540b36ca7c33b442a74abf414360fed8aa0c5c74a8824b42804b1a779c", | |
| "generator_source_files": [ | |
| "simulator/__init__.py", | |
| "simulator/__main__.py", | |
| "simulator/assets.py", | |
| "simulator/atomic_io.py", | |
| "simulator/cli.py", | |
| "simulator/config.py", | |
| "simulator/dataset_files.py", | |
| "simulator/dataset_state.py", | |
| "simulator/demography.py", | |
| "simulator/empirical_maps.py", | |
| "simulator/map_cache.py", | |
| "simulator/maps.py", | |
| "simulator/ne_templates.py", | |
| "simulator/noise.py", | |
| "simulator/replacement.py", | |
| "simulator/replacement_pool.py", | |
| "simulator/sample.py", | |
| "simulator/shards.py", | |
| "simulator/shared_maps.py", | |
| "simulator/slurm.py", | |
| "simulator/stdpopsim_support.py", | |
| "simulator/stdpopsim_templates.py", | |
| "simulator/utils.py" | |
| ], | |
| "git_commit": null | |
| }, | |
| "runtime_environment_sha256": "f849141fba900e44ac7dc4072e8b29f6a04f5474050c0a9c4067f9f890853ce2", | |
| "bench_v2_noise_overlay": { | |
| "schema": "bench_h2h.noise_overlay_plan/1", | |
| "kind": "gen_v3_noise_overlay_on_clean_constant_rows", | |
| "purpose": "benchmark v2 arm A2: A1 baseline rates + gen-v3 production sequencing noise, paired with A1", | |
| "source": { | |
| "dataset_root": "$WORK/bench_h2h_20260915/data/v2_a1_Constant", | |
| "dataset_id": "v2_a1_Constant", | |
| "plan_sha256": "9dcbadba06bd4b48ab40b32e11d9f75b50edb177400d3970f9beaf2d2cf0d89e", | |
| "plan_file_sha256": "0f1c7a51d94b63c2edfcf59ed80645add6693bdf07703385c7fb8d375c29eb6b", | |
| "fragments": [ | |
| { | |
| "chunk": 0, | |
| "receipt_sha256": "4ca84578d8e765fe4737e87ffb3ac09a0be2e6dccd0f7b8cd76b82bd271dc95f", | |
| "npz_sha256": "62a69c6de84c5f273d41f800fcbed5ec2159a3888ff57f6ea2f7be7478ae91cc", | |
| "metadata_sha256": "101283f090990a7f60b2e477ee6e6c98b9948d9b784ebf65e81e88fecae1d857" | |
| }, | |
| { | |
| "chunk": 1, | |
| "receipt_sha256": "0fd67c0fc246e11604e9dff85e0c96da609596d61533f2cb9818bf8ff9972e63", | |
| "npz_sha256": "b4d463cd9f07e06f176b02daa62c2bc2c1d18fb53bba323ee5274880afd87941", | |
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| { | |
| "chunk": 2, | |
| "receipt_sha256": "e106b98b335de354ff1e536f756edea997dc0e8e6795220c13490607afa5e6c2", | |
| "npz_sha256": "6047052a0f66b366c507ee9dc12565e162ac308408d751c153ca0abbd4e7e099", | |
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| } | |
| ] | |
| }, | |
| "target_dataset_id": "v2_a2_Constant", | |
| "generator": { | |
| "root": "$DATA/DLCoalSim/gen-deploy-20260822-tolerance-v3", | |
| "generator_source_sha256": "fc79da540b36ca7c33b442a74abf414360fed8aa0c5c74a8824b42804b1a779c", | |
| "file_sha256": { | |
| "simulator/noise.py": "c049ac4d0a397e4e51ade4f88a5bcf84ff96687e4c7e776f2e1e8e817913e7ac", | |
| "simulator/sample.py": "39dc7f3cfe355b09d0303960837753d6afc7055914150ba9246bd22b7da43d19", | |
| "simulator/config.py": "674ad3b5884aadd22247cf5355b9b667e409c456f5e8421724970cf606ba2290", | |
| "simulator/utils.py": "05d44257f9efedeba69f63c29538c3ca3fd753546dd32b93a2e5e56d23a18652" | |
| } | |
| }, | |
| "noise": { | |
| "profile": "mild_noise", | |
| "order": [ | |
| "noise.noise_params_for_sample", | |
| "noise.add_false_variants", | |
| "noise.apply_genotype_noise[apply_phase_switch_errors -> genotype flips -> missing calls]", | |
| "noise.pack_haplotypes", | |
| "positions rint->uint32" | |
| ], | |
| "source_argument": "bench_v2_noise_overlay", | |
| "ranges": { | |
| "genotype_error_min": 0.001, | |
| "genotype_error_max": 0.004, | |
| "false_variant_rate_per_bp_min": 1.5e-05, | |
| "false_variant_rate_per_bp_max": 0.0006, | |
| "missing_rate_min": 0.002, | |
| "missing_rate_max": 0.02, | |
| "phase_switch_rate_per_het_min": 0.002, | |
| "phase_switch_rate_per_het_max": 0.02 | |
| }, | |
| "rows": "every row, decoys included" | |
| }, | |
| "rng": { | |
| "rule": "entropy = int.from_bytes(sha256(salt + b'|' + source_plan_sha256 + b'|' + '%08d' % sample_index), 'big'); rng = numpy.random.Generator(PCG64(SeedSequence(entropy)))", | |
| "salt": "bench_h2h.noise_overlay.rng/1", | |
| "numpy_version": "2.4.6" | |
| }, | |
| "changed_members": [ | |
| "variant_positions_bp", | |
| "variant_offsets", | |
| "genotype_packed", | |
| "missing_flat_idx", | |
| "missing_offsets", | |
| "missing_storage" | |
| ], | |
| "changed_metadata_keys": [ | |
| "noise_profile", | |
| "n_variants", | |
| "variant_density_per_mb", | |
| "genotype_error", | |
| "missing_rate", | |
| "n_missing_genotypes", | |
| "missing_storage", | |
| "phase_switch_pair_count", | |
| "phaseable_pair_count", | |
| "noise", | |
| "scenario_key", | |
| "generator_recipe_key" | |
| ], | |
| "truth": "unchanged (target_log10_ne, genealogy summaries, observed maps, scenario CSV)", | |
| "receipt_result": "source generation timings kept; slowest_n_variants and fragment_bytes updated", | |
| "tool_sha256": { | |
| "bench_h2h/noise_overlay.py": "0df841ea787224a9714121123b03d96d926aad7b4b8abecf2edbdf25268c7d03", | |
| "bench_h2h/real/dataset_root.py": "4db57250a9596fb1935111f23b5ec5ab01aca471231d6ce607429d9ccef6855d" | |
| } | |
| }, | |
| "plan_sha256": "70a4dd8cc04e46ebde5395150c209ae743b3045dec6be3b9e59f5a696f482d1f" | |
| } | |