diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/envlock_check_51934790.json b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/envlock_check_51934790.json new file mode 100644 index 0000000000000000000000000000000000000000..ca58b515ecc412889b7ebefec9c425939970a24f --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/envlock_check_51934790.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-07", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51934790", + "status": "PASS", + "utc": "20260916T112738Z" +} diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fit_spec.json b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..52ac4c8f29d0d0d9ffe6e2345222b8835cb3431a --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_AGRI_X10_1K", + "g": 1, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_AGRI_X10_1K/r00000001/n32" + ], + "rep": 1, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..8add23dea6730c5d7955c00b471961a0438dec72 --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +26415 8441 5148 3865 2961 2477 2059 1782 1570 1390 1357 1295 1238 1136 966 886 841 815 708 727 738 665 620 596 536 534 518 475 445 443 402 420 437 432 443 351 370 400 332 365 338 330 343 347 296 322 290 343 300 309 288 339 270 259 248 283 265 242 307 304 271 252 229 \ No newline at end of file diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..1275767cc1c1b6d99187635817c312d542dca089 --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_AGRI_X10_1K/K1/g1/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_AGRI_X10_1K/K1/g1/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 1 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..881d63552c2375f0e670fb54e60f3b30a8eb645a --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 11,614 changeTypes: 0 +maxLogL = -3069.513298938472 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 82,925 changeTypes: 2 +standardTime: 0.0226907246929438 generations: 1072.82 N: 9,742 changeTypes: 0 +maxLogL = -341.3162001067067 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 91,692 changeTypes: 1 +standardTime: 0.002681852934870868 generations: 491.81 N: 12,222 changeTypes: 1 +standardTime: 0.05618854271440248 generations: 1799.73 N: 9,671 changeTypes: 0 +maxLogL = -337.58421339073584 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 82,925 changeTypes: 2 +standardTime: 0.0226907246929438 generations: 1072.82 N: 9,742 changeTypes: 0 +maxLogL = -341.3162001067067 + +computing time = 141.25 seconds diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fitcoal/output.txt b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..cf567e856cef393bcaf81bccb045459c7546e47e --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 9742 +4000000 9742 + diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/receipt_51934790.json b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/receipt_51934790.json new file mode 100644 index 0000000000000000000000000000000000000000..b28bdf7f2830028c6e35aa8234cbacc9128b8277 --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/receipt_51934790.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "32f50b11a37c5301d683cc34c8354f7d0974e7ffca39bd961c2212320923f57d", + "elapsed_s": 202, + "failure_sha256": null, + "host": "cn604-07", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51934790", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "e1a318a7cee6e1dae93a419868744ec314bde1b52262cd4cbba7f194a31e4091", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:30:12Z" +} diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/submissions.jsonl b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..60b9271898f449cf5d41fb611a7d5ef8e7d1b0f2 --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g1/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_AGRI_X10_1K/K1/g1/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_AGRI_X10_1K/receipts/export_51933133.json"], "job_id": "51934790", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_AGRI_X10_1K/fitcoal_g1.json", "request_sha256": "525f5f0776a3fc8ef30d3f6c3c32f819684c489cb085a94a8a357956a7cda6da", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [1], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "e1a318a7cee6e1dae93a419868744ec314bde1b52262cd4cbba7f194a31e4091", "stage": "v2", "usage_before": {"account_jobs": 156, "bench_cores": 320, "bench_gpus": 20, "bench_jobs": 85, "bench_pending": 19, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:26:48Z"} diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/envlock_check_51934791.json b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/envlock_check_51934791.json new file mode 100644 index 0000000000000000000000000000000000000000..077bae0f6eb34581bcbcee8b38627ef2eb64753c --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/envlock_check_51934791.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-15", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51934791", + "status": "PASS", + "utc": "20260916T112658Z" +} diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fit_spec.json b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..b996900f0f6fc0c883ba9fef08fe7ae9e344844d --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_AGRI_X10_1K", + "g": 2, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_AGRI_X10_1K/r00000002/n32" + ], + "rep": 2, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..23d567f8c61a4add0ad8792011dc5bd5f26e7291 --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +27142 8647 5058 3771 3058 2480 2158 1863 1758 1479 1422 1200 1193 1095 969 870 881 800 738 730 699 642 616 638 557 581 506 497 538 434 500 444 438 416 470 383 402 438 408 424 363 341 382 341 346 317 323 359 319 337 350 314 282 287 318 332 283 303 258 271 269 290 250 \ No newline at end of file diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..d1096c2ca360cb72087426114b6806387be30953 --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_AGRI_X10_1K/K1/g2/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_AGRI_X10_1K/K1/g2/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 2 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..1ce91d896cda7ce50a621e3b9d50daff57b443e7 --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 11,925 changeTypes: 0 +maxLogL = -3134.416889269254 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 54,884 changeTypes: 1 +standardTime: 0.006814006109803992 generations: 747.96 N: 10,052 changeTypes: 0 +maxLogL = -333.6306095088248 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 86,752 changeTypes: 2 +standardTime: 0.02362091232669031 generations: 1133.30 N: 9,738 changeTypes: 1 +standardTime: 1.9989993429851771 generations: 39604.05 N: 12,085 changeTypes: 0 +maxLogL = -322.8422597307465 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 54,884 changeTypes: 1 +standardTime: 0.006814006109803992 generations: 747.96 N: 10,052 changeTypes: 0 +maxLogL = -333.6306095088248 + +computing time = 146.73 seconds diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fitcoal/output.txt b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..b783f01629eac4a09d9bfc790c6e18e31454f157 --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 10052 +4000000 10052 + diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/receipt_51934791.json b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/receipt_51934791.json new file mode 100644 index 0000000000000000000000000000000000000000..c6305da9f795445f9701464e74394f06f497dfbf --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/receipt_51934791.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "3a2f8f8fadf82987a7cba847af3b4906b7037658ec4860c11862859a0647d103", + "elapsed_s": 159, + "failure_sha256": null, + "host": "cn604-15", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51934791", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "88e6ee25059f49a3f9ef408235b40b87f111505974ac7ed1fdd4e14a9fa8bc40", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:29:35Z" +} diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/submissions.jsonl b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..d8f00508f6ed66588138eb88489074320dda5cad --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g2/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_AGRI_X10_1K/K1/g2/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_AGRI_X10_1K/receipts/export_51933133.json"], "job_id": "51934791", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_AGRI_X10_1K/fitcoal_g2.json", "request_sha256": "1930cd9b9b1a828afad871c1e6737c1598d1bd36e99676a71089def780c6ae8b", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [2], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "88e6ee25059f49a3f9ef408235b40b87f111505974ac7ed1fdd4e14a9fa8bc40", "stage": "v2", "usage_before": {"account_jobs": 157, "bench_cores": 322, "bench_gpus": 20, "bench_jobs": 86, "bench_pending": 19, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:26:52Z"} diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fit_spec.json b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..09cecf77b9d0f8fdd89497cfa5c9bc73aa840e0d --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_AGRI_X10_1K", + "g": 4, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_AGRI_X10_1K/r00000004/n32" + ], + "rep": 4, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..4a68992dbe4060487c553a6931783a66f7bc0c91 --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +26285 8465 5314 3944 3000 2597 2006 1854 1730 1504 1348 1284 1092 1097 1006 943 882 808 777 761 810 692 612 656 590 597 583 628 584 536 465 436 501 496 487 435 390 355 384 368 361 299 381 370 343 307 323 306 310 270 260 334 271 298 284 256 232 264 235 232 276 213 204 \ No newline at end of file diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..4a64ff4876e2a04c7e25e2a01bcb7f1464a5a6d9 --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_AGRI_X10_1K/K1/g4/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_AGRI_X10_1K/K1/g4/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 4 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..4ca9b6e8986abdaa1b43809e2a20df1363117857 --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 11,834 changeTypes: 0 +maxLogL = -2741.9616399537917 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 97,919 changeTypes: 2 +standardTime: 0.018341571101470538 generations: 938.79 N: 10,106 changeTypes: 0 +maxLogL = -337.37107374096206 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 1,152,996 changeTypes: 2 +standardTime: 0.004242223720814924 generations: 530.14 N: 13,991 changeTypes: 1 +standardTime: 0.033121541334423014 generations: 1338.25 N: 10,060 changeTypes: 0 +maxLogL = -334.5179632390111 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 97,919 changeTypes: 2 +standardTime: 0.018341571101470538 generations: 938.79 N: 10,106 changeTypes: 0 +maxLogL = -337.37107374096206 + +computing time = 146.81 seconds diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fitcoal/output.txt b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..024facd0a0b25c92147a528d82b0cb6e61eb443e --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 10106 +4000000 10106 + diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/receipt_51934798.json b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/receipt_51934798.json new file mode 100644 index 0000000000000000000000000000000000000000..089d61775c68895d49bbdb2f6e5c614553deb3bb --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g4/n32/receipt_51934798.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "c4b1bd7ddf13fd3f32e4e12601e0a1bfdec128a3cab5db21aa07c99edaeafc29", + "elapsed_s": 164, + "failure_sha256": null, + "host": "cn604-03", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51934798", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "bca2e426d4a2c8b96595c20fb2555c157ad9f46fc2b9815461ef04f6d8e79a63", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:29:51Z" +} diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/envlock_check_51934801.json b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/envlock_check_51934801.json new file mode 100644 index 0000000000000000000000000000000000000000..30b6b2461d481599deae72dc022775c45a126b59 --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/envlock_check_51934801.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-02", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51934801", + "status": "PASS", + "utc": "20260916T112757Z" +} diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fit_spec.json b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..ea8dc340d378cc370076d77ad30308dcc88154eb --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_AGRI_X10_1K", + "g": 7, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_AGRI_X10_1K/r00000007/n32" + ], + "rep": 7, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..6f533e994513b51a7732d2c85669719c146e5536 --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +27007 8507 5286 3722 2868 2466 2149 1799 1565 1356 1375 1266 1135 1060 1002 956 894 837 755 756 724 716 652 581 665 557 542 558 503 502 493 423 471 443 398 408 415 348 450 369 402 325 402 344 309 293 328 338 348 293 276 292 302 277 245 276 266 239 257 249 304 251 204 \ No newline at end of file diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..8d8d067bc18617a78b052b1e5c53aef671f2e723 --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_AGRI_X10_1K/K1/g7/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_AGRI_X10_1K/K1/g7/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 3 -randSeed 7 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..e7b5d92f75bc962d1e7ce012059dfe410c81c3fb --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 11,829 changeTypes: 0 +maxLogL = -3140.9418884611555 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 97,052 changeTypes: 2 +standardTime: 0.02076467033946912 generations: 1045.34 N: 9,903 changeTypes: 0 +maxLogL = -303.040188812545 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 83,812 changeTypes: 2 +standardTime: 0.024271443211634304 generations: 1144.74 N: 9,655 changeTypes: 1 +standardTime: 0.431933690956922 generations: 9016.71 N: 10,049 changeTypes: 0 +maxLogL = -300.8977430537859 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 97,052 changeTypes: 2 +standardTime: 0.02076467033946912 generations: 1045.34 N: 9,903 changeTypes: 0 +maxLogL = -303.040188812545 + +computing time = 153.25 seconds diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fitcoal/output.txt b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..2061e788fb419647d05666d45c6271c43852a003 --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 9903 +4000000 9903 + diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..47de88aebecef4006ba97a94faaf20de764f8f92 --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 3 (recommended) +The proportion of truncated or collapsed SFS types: 0.047619047619047616 + diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/receipt_51934801.json b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/receipt_51934801.json new file mode 100644 index 0000000000000000000000000000000000000000..9074f91c48adb991f72e8246aca108b5f427d6ae --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/receipt_51934801.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "17071e34a2bdae3f801b6b924e54f9d9b696f902286c6fd5c6d23d8de9c75dbd", + "elapsed_s": 194, + "failure_sha256": null, + "host": "cn604-02", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51934801", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "8d389fe6ae76bb3fbb59d00ffff54fb2b7b3435c9f27827a242ec48626f90678", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:30:39Z" +} diff --git a/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/submissions.jsonl b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..b5cb76970ac89d44bba2c0cf29043b2e0e913367 --- /dev/null +++ b/estimates/fitcoal/a1/AGRI_X10_1K/K1/g7/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_AGRI_X10_1K/K1/g7/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_AGRI_X10_1K/receipts/export_51933133.json"], "job_id": "51934801", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_AGRI_X10_1K/fitcoal_g7.json", "request_sha256": "d81353f9972cf5a5dd1e24aabf1a01386207f3b812f5d9a38469460284a18307", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [7], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "8d389fe6ae76bb3fbb59d00ffff54fb2b7b3435c9f27827a242ec48626f90678", "stage": "v2", "usage_before": {"account_jobs": 159, "bench_cores": 320, "bench_gpus": 20, "bench_jobs": 88, "bench_pending": 19, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:27:23Z"} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/envlock_check_51944131.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/envlock_check_51944131.json new file mode 100644 index 0000000000000000000000000000000000000000..4624fd9ede90ddc7981eb72dcfeaf6b8504a67e8 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/envlock_check_51944131.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-03", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51944131", + "status": "PASS", + "utc": "20260916T123734Z" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fit_spec.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..89bfa088711e63bc106b13174627c3f5352b70af --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_ANCIENT_GROWTH_X10", + "g": 0, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_ANCIENT_GROWTH_X10/r00000000/n32" + ], + "rep": 0, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..2ec58ef8bc3e680948ee43e3beaad098417179c0 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +43769 21967 14322 10946 8385 6986 6069 5177 4767 4114 3710 3384 2986 2904 2591 2517 2314 2220 2006 1920 1774 1641 1551 1578 1327 1489 1339 1235 1182 1079 1163 1046 990 1041 954 893 854 891 855 817 754 729 722 658 659 626 632 642 669 678 528 556 562 526 569 482 485 480 453 443 481 460 430 \ No newline at end of file diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..49ac6a496b92e7f00ebe36be3c93a762cf0a7dca --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g0/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g0/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 0 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..d1819fb8665cdcb4af4da27c3afdfe1dae57c55d --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 26,786 changeTypes: 0 +maxLogL = -1683.1611383258114 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 29,594 changeTypes: 1 +standardTime: 1.2614198646633672 generations: 74660.62 N: 13,484 changeTypes: 0 +maxLogL = -343.7415991620496 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 29,367 changeTypes: 1 +standardTime: 0.36880367683329085 generations: 21661.23 N: 38,793 changeTypes: 2 +standardTime: 1.4577690792266136 generations: 75132.79 N: 16,507 changeTypes: 0 +maxLogL = -341.01185920498165 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 29,594 changeTypes: 1 +standardTime: 1.2614198646633672 generations: 74660.62 N: 13,484 changeTypes: 0 +maxLogL = -343.7415991620496 + +computing time = 218.24 seconds diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fitcoal/output.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..91dcdc09fac571f6d75e6ab8961be8dbfee0cadd --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 29594 +74661 29594 +74661 13484 +4000000 13484 + diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/receipt_51944131.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/receipt_51944131.json new file mode 100644 index 0000000000000000000000000000000000000000..507ae95b4868594e19dda741427ea77114202a4a --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/receipt_51944131.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "150e98535e8c3a2884912dd60cb4c87197019d6f13196d780e9e59f96f4eb0e1", + "elapsed_s": 265, + "failure_sha256": null, + "host": "cn604-03", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51944131", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "d464ea6c7c28d9607774d45c4c2ce259ae8c191cc42ae4e924574a4b97e133cd", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:41:24Z" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/submissions.jsonl b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..09d64a473b359dce7b4e9a08184713adb0048677 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g0/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g0/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_ANCIENT_GROWTH_X10/receipts/export_51933466.json"], "job_id": "51944131", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_ANCIENT_GROWTH_X10/fitcoal_g0.json", "request_sha256": "a71c9826f4099b5896fa48dc3e20adf8ffe8ce0e9e391e8f2c399acc479e1072", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [0], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "d464ea6c7c28d9607774d45c4c2ce259ae8c191cc42ae4e924574a4b97e133cd", "stage": "v2", "usage_before": {"account_jobs": 188, "bench_cores": 737, "bench_gpus": 18, "bench_jobs": 135, "bench_pending": 41, "never_startable_pending": 0, "throttle_held_not_counted": 23}, "utc": "2026-09-16T12:36:49Z"} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/envlock_check_51944156.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/envlock_check_51944156.json new file mode 100644 index 0000000000000000000000000000000000000000..0446a2837a8516a7205d89a88c6cd93ca5248bc9 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/envlock_check_51944156.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-03", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51944156", + "status": "PASS", + "utc": "20260916T123742Z" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fit_spec.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..6c9abe850e6f888c5ef586b4208849b56a107eba --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_ANCIENT_GROWTH_X10", + "g": 1, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_ANCIENT_GROWTH_X10/r00000001/n32" + ], + "rep": 1, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..bc024d94cfc4da3cf1882559ed474d07628acde6 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +46137 22134 14489 10637 8634 7266 6072 5122 4428 4036 3584 3324 3002 2855 2723 2469 2274 2160 2003 1873 1716 1659 1610 1522 1411 1470 1283 1328 1119 1080 1129 1029 1016 971 892 954 870 864 863 761 816 757 750 702 715 689 655 627 671 605 563 528 587 521 503 463 484 519 486 389 503 429 470 \ No newline at end of file diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..8e43b5dbec71f4de2ae24eb32388e2d6e0578080 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g1/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g1/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 1 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..f36123dc5f648ee36c0e4cb34da44dfeb03169e7 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 27,100 changeTypes: 0 +maxLogL = -1944.3666445332253 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 30,489 changeTypes: 1 +standardTime: 0.8418714091255723 generations: 51335.28 N: 17,762 changeTypes: 0 +maxLogL = -359.2192209797497 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 35,859 changeTypes: 1 +standardTime: 0.008201886669740015 generations: 588.23 N: 29,751 changeTypes: 1 +standardTime: 1.055919573693724 generations: 62930.47 N: 15,969 changeTypes: 0 +maxLogL = -341.240931990151 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 30,489 changeTypes: 1 +standardTime: 0.8418714091255723 generations: 51335.28 N: 17,762 changeTypes: 0 +maxLogL = -359.2192209797497 + +computing time = 195.96 seconds diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fitcoal/output.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..3662f7c4b25c53ce99ea533cfc2527f21d2257c1 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 30489 +51335 30489 +51335 17762 +4000000 17762 + diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/receipt_51944156.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/receipt_51944156.json new file mode 100644 index 0000000000000000000000000000000000000000..ecf438be983253c1bb74fc2a4de296ae703369bc --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/receipt_51944156.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "4dcb6e3c6912e24400dc7bd71b0ff84372feb5563b6cb625a467c8f1d634ae90", + "elapsed_s": 251, + "failure_sha256": null, + "host": "cn604-03", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51944156", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "a43b027d854e4bfdd4ead626fbafe0a20de1707de0a47cf1678bbe3eae197937", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:41:10Z" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/submissions.jsonl b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..c2ee7da4a4ff71c9e376ca3a3f111796239f08a1 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g1/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g1/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_ANCIENT_GROWTH_X10/receipts/export_51933466.json"], "job_id": "51944156", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_ANCIENT_GROWTH_X10/fitcoal_g1.json", "request_sha256": "e5b4526bc7479a7a2e25eed0b7ae994d543a6983f2f95f28ea51e85ae874d5f3", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [1], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "a43b027d854e4bfdd4ead626fbafe0a20de1707de0a47cf1678bbe3eae197937", "stage": "v2", "usage_before": {"account_jobs": 188, "bench_cores": 739, "bench_gpus": 18, "bench_jobs": 135, "bench_pending": 42, "never_startable_pending": 0, "throttle_held_not_counted": 22}, "utc": "2026-09-16T12:36:57Z"} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/envlock_check_51944295.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/envlock_check_51944295.json new file mode 100644 index 0000000000000000000000000000000000000000..c34751cb219b8eed6a7a776b685a7807f70ab2cf --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/envlock_check_51944295.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn113-35-l", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51944295", + "status": "PASS", + "utc": "20260916T123803Z" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fit_spec.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..275d839a42ccd446da94e4bf716f8ced4b8152d9 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_ANCIENT_GROWTH_X10", + "g": 2, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_ANCIENT_GROWTH_X10/r00000002/n32" + ], + "rep": 2, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..c4f0f0fae115f0d86145ffb7299b50840ed2afec --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +45039 21968 14231 10866 8642 6948 5876 5358 4673 4103 3649 3280 3030 2795 2638 2506 2380 2224 1869 1837 1810 1658 1624 1577 1494 1318 1349 1217 1247 1181 1140 1089 1050 996 975 915 891 858 858 779 761 778 749 694 724 615 677 630 570 560 587 563 518 507 502 551 504 444 484 432 398 429 368 \ No newline at end of file diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..79ad035e3765e7d04edda9be8bf7308d48b65a78 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g2/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g2/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 2 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..e04b02c0ceb7c86a06480bb8fa24c04337124312 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 26,928 changeTypes: 0 +maxLogL = -1848.0123824562368 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 29,861 changeTypes: 1 +standardTime: 1.3842963563233561 generations: 82672.46 N: 10,828 changeTypes: 0 +maxLogL = -338.29410345304336 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 32,781 changeTypes: 1 +standardTime: 0.009918943608780406 generations: 650.30 N: 29,430 changeTypes: 1 +standardTime: 1.885952720946765 generations: 111074.25 N: 509 changeTypes: 0 +maxLogL = -330.12747158398133 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 29,861 changeTypes: 1 +standardTime: 1.3842963563233561 generations: 82672.46 N: 10,828 changeTypes: 0 +maxLogL = -338.29410345304336 + +computing time = 391.17 seconds diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fitcoal/output.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..7a57c4def979bd91bae211c6bbf4aff65a64ef8d --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 29861 +82672 29861 +82672 10828 +4000000 10828 + diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/receipt_51944295.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/receipt_51944295.json new file mode 100644 index 0000000000000000000000000000000000000000..cd5d9cf70fc640e3879c1819cc85239978d35626 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/receipt_51944295.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "40250390266182cdda2f0ee4a5cb3be0fde39c1f7b6eef6d940c75ea3589ef81", + "elapsed_s": 415, + "failure_sha256": null, + "host": "cn113-35-l", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51944295", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "2ef801744db8b002bf2d81d762587e750012b26db24cffb470618ef0c7dca850", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:44:50Z" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/submissions.jsonl b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..5bee6126348012f016fcb2d198a4241bcb9c7add --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g2/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g2/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_ANCIENT_GROWTH_X10/receipts/export_51933466.json"], "job_id": "51944295", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_ANCIENT_GROWTH_X10/fitcoal_g2.json", "request_sha256": "823c09b06554dbf41567a2533403d651fe74cde7891f422591424e88d641a0ad", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [2], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "2ef801744db8b002bf2d81d762587e750012b26db24cffb470618ef0c7dca850", "stage": "v2", "usage_before": {"account_jobs": 188, "bench_cores": 805, "bench_gpus": 18, "bench_jobs": 135, "bench_pending": 23, "never_startable_pending": 0, "throttle_held_not_counted": 22}, "utc": "2026-09-16T12:37:52Z"} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/envlock_check_51944350.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/envlock_check_51944350.json new file mode 100644 index 0000000000000000000000000000000000000000..9c1ac877df6d65329173e8324102a775cf12faf1 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/envlock_check_51944350.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn113-35-l", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51944350", + "status": "PASS", + "utc": "20260916T123823Z" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fit_spec.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..c3ab60ec9f310ca53abeb7634ffb7918341e9463 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_ANCIENT_GROWTH_X10", + "g": 3, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_ANCIENT_GROWTH_X10/r00000003/n32" + ], + "rep": 3, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..6eec0e6ac4ad47fa9d074ae3fef0ddfc56a0cf2c --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +41499 21833 14643 10436 8627 7160 6221 5359 4838 4170 3747 3459 3066 2874 2695 2380 2138 2212 2047 1870 1801 1722 1548 1547 1374 1495 1337 1292 1180 1154 1144 1168 1017 987 941 884 963 873 769 844 813 811 735 677 715 677 629 628 659 597 573 566 543 495 537 560 522 501 490 417 419 411 354 \ No newline at end of file diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..2f793bd698c527de450e49a3d0ae52ea8bdb5abc --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g3/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g3/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 3 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..ae5c281a7172147d7a906e3a4576876cebade6ef --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 26,598 changeTypes: 0 +maxLogL = -1544.8281983156107 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 29,041 changeTypes: 1 +standardTime: 1.9793953382414213 generations: 114966.39 N: 290 changeTypes: 0 +maxLogL = -409.4794096050298 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 9,483 changeTypes: 2 +standardTime: 0.004741565623754727 generations: 150.96 N: 29,764 changeTypes: 1 +standardTime: 1.6848874499114774 generations: 100167.91 N: 5,690 changeTypes: 0 +maxLogL = -353.5048901897171 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 29,041 changeTypes: 1 +standardTime: 1.9793953382414213 generations: 114966.39 N: 290 changeTypes: 0 +maxLogL = -409.4794096050298 + +computing time = 369.16 seconds diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fitcoal/output.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..87a48e7c55bf5bca0a707c70d537b9415c154e77 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 29041 +114966 29041 +114966 290 +4000000 290 + diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/receipt_51944350.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/receipt_51944350.json new file mode 100644 index 0000000000000000000000000000000000000000..a6629ce04d430d612cc7d88c866a60cf1628f414 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/receipt_51944350.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "7582a7041db86fefdafd232085b24f29ff1950dc1c5b886b82c3ae4cd12b27e5", + "elapsed_s": 384, + "failure_sha256": null, + "host": "cn113-35-l", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51944350", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "8d83a627c73e7ccf3f84cb12f0b89eb31f813c233f6012d32fc2347c4fb69dd3", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:44:45Z" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/submissions.jsonl b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..fa64b48e3da761a254f6062dc59ebeff4ea84d47 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g3/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g3/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_ANCIENT_GROWTH_X10/receipts/export_51933466.json"], "job_id": "51944350", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_ANCIENT_GROWTH_X10/fitcoal_g3.json", "request_sha256": "b34965a8fa4c2a62c24f05e35a1656c7b7325f9ddd4643b2fe4a6fffbbfc79fc", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [3], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "8d83a627c73e7ccf3f84cb12f0b89eb31f813c233f6012d32fc2347c4fb69dd3", "stage": "v2", "usage_before": {"account_jobs": 182, "bench_cores": 759, "bench_gpus": 18, "bench_jobs": 129, "bench_pending": 22, "never_startable_pending": 0, "throttle_held_not_counted": 21}, "utc": "2026-09-16T12:38:16Z"} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/envlock_check_51944375.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/envlock_check_51944375.json new file mode 100644 index 0000000000000000000000000000000000000000..ebedf68a08fcdfc484e5ccee9172d636a426aec6 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/envlock_check_51944375.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn113-35-l", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51944375", + "status": "PASS", + "utc": "20260916T123837Z" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fit_spec.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..5d07f122cbffa969c4a06678776171e70dccf2d3 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_ANCIENT_GROWTH_X10", + "g": 4, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_ANCIENT_GROWTH_X10/r00000004/n32" + ], + "rep": 4, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..4450f1aeef0cf995b02e4f22464dcd09530fcf26 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +44924 22192 14770 10819 8373 6938 6275 5151 4611 4028 3635 3413 3041 2718 2524 2498 2440 2108 2077 1864 1772 1679 1631 1593 1417 1260 1309 1215 1232 1151 1143 1132 1025 969 955 911 840 763 795 889 810 762 676 680 678 673 696 633 612 654 561 519 502 589 491 465 503 470 494 448 405 430 407 \ No newline at end of file diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..39b06e83ee97de5c18a69206428de1794b544a58 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g4/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g4/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 4 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..11c191419f24a298ce71299329dfbb616e5e2c74 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 26,964 changeTypes: 0 +maxLogL = -1909.098093462325 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 30,074 changeTypes: 1 +standardTime: 1.1069435785079549 generations: 66579.36 N: 14,797 changeTypes: 0 +maxLogL = -357.4941197834314 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 30,448 changeTypes: 1 +standardTime: 0.11158451960946712 generations: 6795.00 N: 29,288 changeTypes: 1 +standardTime: 1.5187347416329833 generations: 89219.64 N: 9,236 changeTypes: 0 +maxLogL = -354.4501779595364 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 30,074 changeTypes: 1 +standardTime: 1.1069435785079549 generations: 66579.36 N: 14,797 changeTypes: 0 +maxLogL = -357.4941197834314 + +computing time = 452.18 seconds diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fitcoal/output.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..3a050a9b120f9b34e57b85f281c7f406f0597536 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 30074 +66579 30074 +66579 14797 +4000000 14797 + diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/receipt_51944375.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/receipt_51944375.json new file mode 100644 index 0000000000000000000000000000000000000000..c7b7daeb524ec949fd7ec76392065de7a2869266 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/receipt_51944375.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "ff951b576f77619443b33ca42b528f12551c98e9a3aa2c82a131684fb06fc23e", + "elapsed_s": 467, + "failure_sha256": null, + "host": "cn113-35-l", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51944375", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "6ecfd8ea4947f743cd9e0bdd1a2a65dbf13e12fa0c7ba465f837fa953e6a04ef", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:46:22Z" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/submissions.jsonl b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..840e8dffd7eae658b07870b3cb51932c1dae4df1 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g4/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g4/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_ANCIENT_GROWTH_X10/receipts/export_51933466.json"], "job_id": "51944375", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_ANCIENT_GROWTH_X10/fitcoal_g4.json", "request_sha256": "644c381417dbb7591015823e37722aceb957b2d82633e5ac9a403e6d3bebb755", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [4], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "6ecfd8ea4947f743cd9e0bdd1a2a65dbf13e12fa0c7ba465f837fa953e6a04ef", "stage": "v2", "usage_before": {"account_jobs": 181, "bench_cores": 721, "bench_gpus": 18, "bench_jobs": 128, "bench_pending": 22, "never_startable_pending": 0, "throttle_held_not_counted": 20}, "utc": "2026-09-16T12:38:33Z"} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/envlock_check_51944396.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/envlock_check_51944396.json new file mode 100644 index 0000000000000000000000000000000000000000..6234e66a94c1ac0e092ddc0412b6a1ff42239324 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/envlock_check_51944396.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-14", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51944396", + "status": "PASS", + "utc": "20260916T123854Z" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fit_spec.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..7bf39a843ad99780be2c21ccf0c3c66ef125621d --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_ANCIENT_GROWTH_X10", + "g": 5, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_ANCIENT_GROWTH_X10/r00000005/n32" + ], + "rep": 5, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..52825e1e0efc22aba79dd932f48a5c9cce1388df --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +44266 22274 14752 10816 8502 7050 5971 5121 4561 4042 3671 3407 3081 2736 2579 2409 2301 2137 2001 1826 1729 1727 1503 1505 1467 1333 1396 1275 1205 1092 1071 1000 993 990 984 852 933 823 831 766 742 723 697 716 736 646 709 597 669 588 563 526 542 548 499 487 530 496 451 401 442 473 422 \ No newline at end of file diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..4883629722fa4aeae6de98095b4695c25dbac978 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g5/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g5/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 5 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..0037afd8db21c51f04ca97ffa415d86e6fb840f0 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 26,815 changeTypes: 0 +maxLogL = -1842.7789876854483 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 29,955 changeTypes: 1 +standardTime: 1.0001840301814613 generations: 59920.89 N: 16,103 changeTypes: 0 +maxLogL = -330.676223919598 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 24,202 changeTypes: 2 +standardTime: 0.0028894627490789276 generations: 155.67 N: 30,101 changeTypes: 1 +standardTime: 0.9551577134111979 generations: 57484.41 N: 16,503 changeTypes: 0 +maxLogL = -329.6126998567431 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 29,955 changeTypes: 1 +standardTime: 1.0001840301814613 generations: 59920.89 N: 16,103 changeTypes: 0 +maxLogL = -330.676223919598 + +computing time = 203.64 seconds diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fitcoal/output.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..2d30156b553dc07249f496773b98fb0fa3f3624b --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 29955 +59921 29955 +59921 16103 +4000000 16103 + diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/receipt_51944396.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/receipt_51944396.json new file mode 100644 index 0000000000000000000000000000000000000000..ba547c6df2c8d94a1af64eae5c17b299c26cb05d --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/receipt_51944396.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "f26cf8bb8473c8baadd2666d9ba9a7a658aae380b8d9345d950972a9de71df95", + "elapsed_s": 220, + "failure_sha256": null, + "host": "cn604-14", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51944396", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "a00254a3b27d24afe6911123e12b2b26dfad49c037fbcbb05c2463c0eb57a29a", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:42:31Z" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/submissions.jsonl b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..2446c3660896a2f8ad208d78aa39f2b88dfe335c --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g5/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g5/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_ANCIENT_GROWTH_X10/receipts/export_51933466.json"], "job_id": "51944396", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_ANCIENT_GROWTH_X10/fitcoal_g5.json", "request_sha256": "48ad37266b97823088dffd58283a2e6b9e6e0bbed89eeb6ca4ab459fe6e49e8a", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [5], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "a00254a3b27d24afe6911123e12b2b26dfad49c037fbcbb05c2463c0eb57a29a", "stage": "v2", "usage_before": {"account_jobs": 182, "bench_cores": 723, "bench_gpus": 18, "bench_jobs": 129, "bench_pending": 21, "never_startable_pending": 0, "throttle_held_not_counted": 20}, "utc": "2026-09-16T12:38:48Z"} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/envlock_check_51944418.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/envlock_check_51944418.json new file mode 100644 index 0000000000000000000000000000000000000000..6096ae22b165b52f24510dc1dc5ae87ec630f93e --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/envlock_check_51944418.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-10", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51944418", + "status": "PASS", + "utc": "20260916T123905Z" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fit_spec.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..326776f9e82af798a964477b2d3b004b8bd6a137 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_ANCIENT_GROWTH_X10", + "g": 6, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_ANCIENT_GROWTH_X10/r00000006/n32" + ], + "rep": 6, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..9c0de70bd8a8821fe83128cddf97d5fd9df4ca7d --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +44113 21457 14458 10460 8444 6883 5991 5251 4796 4072 3603 3471 3192 2819 2606 2273 2169 2067 1915 1854 1795 1763 1610 1605 1489 1420 1366 1215 1123 1184 1056 1050 1023 1016 944 889 912 900 835 870 858 805 723 735 653 682 618 638 577 611 602 632 542 522 543 422 463 457 497 436 445 425 421 \ No newline at end of file diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..5bb57092a09585747039f60b7cb3e45922f29989 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g6/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g6/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 6 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..f9c3aeefc137cd6769b71d502c6bed2690dd8425 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 26,686 changeTypes: 0 +maxLogL = -1650.87087462327 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 29,376 changeTypes: 1 +standardTime: 1.4462276078523337 generations: 84969.98 N: 10,799 changeTypes: 0 +maxLogL = -357.2390685131031 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 55,005 changeTypes: 2 +standardTime: 0.0014897588266456878 generations: 117.29 N: 29,133 changeTypes: 1 +standardTime: 1.8388449968953577 generations: 107170.80 N: 3,078 changeTypes: 0 +maxLogL = -354.32467855501227 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 29,376 changeTypes: 1 +standardTime: 1.4462276078523337 generations: 84969.98 N: 10,799 changeTypes: 0 +maxLogL = -357.2390685131031 + +computing time = 213.88 seconds diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fitcoal/output.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1a0ba47c67a49e15688cf642f2d845e70789052 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 29376 +84970 29376 +84970 10799 +4000000 10799 + diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/receipt_51944418.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/receipt_51944418.json new file mode 100644 index 0000000000000000000000000000000000000000..ab6c652b8b74835001be0931556be130978a4b8c --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/receipt_51944418.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "2172b7856bb44f5b5f35e78135c26d79848027a1503a3da2ed6e320f701f6b09", + "elapsed_s": 231, + "failure_sha256": null, + "host": "cn604-10", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51944418", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "85bcaaf26b7e748ac322e762b0e80a36e8d61276e81b5822f53da7f40b51f5b0", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:42:53Z" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/submissions.jsonl b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..cdc85ad03fd0a391f8e96540c130f67468dfadb0 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g6/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g6/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_ANCIENT_GROWTH_X10/receipts/export_51933466.json"], "job_id": "51944418", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_ANCIENT_GROWTH_X10/fitcoal_g6.json", "request_sha256": "e6c314065961f0b2683b2f6162d2de00ad651e5aabee258c7444454e5a53f7b6", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [6], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "85bcaaf26b7e748ac322e762b0e80a36e8d61276e81b5822f53da7f40b51f5b0", "stage": "v2", "usage_before": {"account_jobs": 182, "bench_cores": 717, "bench_gpus": 18, "bench_jobs": 129, "bench_pending": 21, "never_startable_pending": 0, "throttle_held_not_counted": 20}, "utc": "2026-09-16T12:38:59Z"} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/envlock_check_51944483.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/envlock_check_51944483.json new file mode 100644 index 0000000000000000000000000000000000000000..34e32af249656aafabfbe2813bd77d7f683dff01 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/envlock_check_51944483.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-04", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51944483", + "status": "PASS", + "utc": "20260916T123918Z" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fit_spec.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..46ff66927565345270379657f4455a15af710f80 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_ANCIENT_GROWTH_X10", + "g": 7, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_ANCIENT_GROWTH_X10/r00000007/n32" + ], + "rep": 7, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..a6ae7d0e3a8880bf2a6b008d5a202ab13fa1f106 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +44296 22277 14533 10494 8607 6949 5965 4992 4471 4000 3503 3242 3034 2714 2557 2393 2233 2159 2007 1922 1752 1608 1548 1572 1408 1441 1232 1244 1186 1152 1149 1059 1052 840 913 920 856 925 810 818 824 802 707 735 754 619 638 549 625 590 552 530 574 521 505 457 501 476 529 493 457 408 425 \ No newline at end of file diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..df1567e7bbcaf420e4566114e48693d0ee95ca19 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g7/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g7/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 7 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..aaf8bb1175bf7c9fd774860f5b9285072bb8d316 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 26,663 changeTypes: 0 +maxLogL = -1796.4664898049527 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 29,780 changeTypes: 1 +standardTime: 0.930341759920167 generations: 55411.20 N: 16,970 changeTypes: 0 +maxLogL = -356.12736599872187 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 30,192 changeTypes: 1 +standardTime: 0.17641047369909296 generations: 10652.49 N: 28,055 changeTypes: 1 +standardTime: 1.783973909362055 generations: 100852.91 N: 6,173 changeTypes: 0 +maxLogL = -349.97546086630246 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 29,780 changeTypes: 1 +standardTime: 0.930341759920167 generations: 55411.20 N: 16,970 changeTypes: 0 +maxLogL = -356.12736599872187 + +computing time = 189.85 seconds diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fitcoal/output.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..38696f1fc1f33650b2116aa15004f3d84f598870 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 29780 +55411 29780 +55411 16970 +4000000 16970 + diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/receipt_51944483.json b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/receipt_51944483.json new file mode 100644 index 0000000000000000000000000000000000000000..9d8d63c88f934d3e24f5bc17b25128a843b68563 --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/receipt_51944483.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "8faf52bc1ebd94acc1b793fec5c0d598a18182629f027f8dceab6fe5cdc75796", + "elapsed_s": 204, + "failure_sha256": null, + "host": "cn604-04", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51944483", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "086f21656319506fcf0eb5ab4108f48d51ba5ac5e17bc02752444bf014795b43", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:42:39Z" +} diff --git a/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/submissions.jsonl b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..88daca37029b9c5bd65e3dde88f038669e5e76fd --- /dev/null +++ b/estimates/fitcoal/a1/ANCIENT_GROWTH_X10/K1/g7/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_ANCIENT_GROWTH_X10/K1/g7/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_ANCIENT_GROWTH_X10/receipts/export_51933466.json"], "job_id": "51944483", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_ANCIENT_GROWTH_X10/fitcoal_g7.json", "request_sha256": "d58d5688898588ee65bcedc5b54233514af6f26d2e33f674eabe34866a4dceeb", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [7], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "086f21656319506fcf0eb5ab4108f48d51ba5ac5e17bc02752444bf014795b43", "stage": "v2", "usage_before": {"account_jobs": 181, "bench_cores": 671, "bench_gpus": 18, "bench_jobs": 128, "bench_pending": 21, "never_startable_pending": 0, "throttle_held_not_counted": 20}, "utc": "2026-09-16T12:39:13Z"} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/envlock_check_51935442.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/envlock_check_51935442.json new file mode 100644 index 0000000000000000000000000000000000000000..a8af4110a6267f0f0f5f41d2ebd976e4de6eedc3 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/envlock_check_51935442.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn605-21-r", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935442", + "status": "PASS", + "utc": "20260916T120045Z" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..701e72f6070b536b4240c8a1208d5aad6eed9598 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X100_5K", + "g": 0, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X100_5K/r00000000/n32" + ], + "rep": 0, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..9fda4215e674a24f726365718c961eb1cdebb2da --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +13459 6201 3739 2498 1832 1270 935 780 650 516 386 329 264 214 182 144 123 94 83 74 69 61 30 36 22 29 16 12 12 15 13 9 8 8 7 4 1 3 4 7 3 4 1 1 1 1 3 0 4 4 2 1 1 0 4 1 1 1 4 2 2 1 1 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..0c273e07db42d73c1c51e48234283ad7a9305df3 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g0/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g0/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 0 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..9478b4b187c6161c176ab9e58d3a3f065868d198 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 4,820 changeTypes: 0 +maxLogL = -11598.152420517637 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 10,180 changeTypes: 1 +standardTime: 0.2437190908821867 generations: 4962.24 N: 102 changeTypes: 0 +maxLogL = -195.14329159407066 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 10,150 changeTypes: 1 +standardTime: 0.24855192934687287 generations: 5045.70 N: 110 changeTypes: 2 +standardTime: 0.2585535956380479 generations: 5047.23 N: 55 changeTypes: 0 +maxLogL = -184.0224436477861 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 10,180 changeTypes: 1 +standardTime: 0.2437190908821867 generations: 4962.24 N: 102 changeTypes: 0 +maxLogL = -195.14329159407066 + +computing time = 301.25 seconds diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..86002f125ffe3d2e38447a93b0de412cdd5f624d --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 10180 +4962 10180 +4962 102 +4000000 102 + diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/receipt_51935442.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/receipt_51935442.json new file mode 100644 index 0000000000000000000000000000000000000000..2141edf78b8db5dd6e0e7b02f6cc38f933e2f7da --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/receipt_51935442.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "98d1482aabaed38cd3a58cd635212b6f1e24f97f29cf9c3a2ed5861c27ee9047", + "elapsed_s": 338, + "failure_sha256": null, + "host": "cn605-21-r", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935442", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "b770e5d61819ac28622e230c8541cce6ce95ed3d343c31f0daef4e67e7fb86ed", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:06:11Z" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..c1be3a048835c309212d53197d6a6115aeab3f61 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g0/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g0/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X100_5K/receipts/export_51933438.json"], "job_id": "51935442", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X100_5K/fitcoal_g0.json", "request_sha256": "4d4c91e4ef044b4085bedfc6d1c3c9596dcd216edcd06d6ee1dd9454a2aa94da", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [0], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "b770e5d61819ac28622e230c8541cce6ce95ed3d343c31f0daef4e67e7fb86ed", "stage": "v2", "usage_before": {"account_jobs": 186, "bench_cores": 573, "bench_gpus": 19, "bench_jobs": 115, "bench_pending": 82, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:36:15Z"} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/envlock_check_51935444.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/envlock_check_51935444.json new file mode 100644 index 0000000000000000000000000000000000000000..c89e701e7952a009001c2c71c6a0efef9b4f1efc --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/envlock_check_51935444.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn605-21-l", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935444", + "status": "PASS", + "utc": "20260916T120037Z" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..a19a89880f8736b26a965438eb84eeb6bd7f4891 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X100_5K", + "g": 1, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X100_5K/r00000001/n32" + ], + "rep": 1, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..44b0d2ac6573c9f64eb0fce6a20401949681ef79 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +13333 6079 3601 2344 1775 1408 966 730 602 512 410 366 274 202 182 165 124 90 79 78 74 52 51 51 27 27 28 21 24 17 10 18 13 5 9 7 8 3 4 5 3 1 5 5 3 6 10 7 3 5 2 3 2 4 7 5 3 3 1 3 2 0 1 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..756c8f5cf15d50603d8a6b391798d9824a75e0d4 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g1/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g1/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 1 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..fde5a1bab882b53874fb1df94f0cffcaa9a3c7a5 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 4,774 changeTypes: 0 +maxLogL = -10955.172190262549 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 9,917 changeTypes: 1 +standardTime: 0.25302780051044 generations: 5018.46 N: 112 changeTypes: 0 +maxLogL = -201.45624462979086 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 8,336 changeTypes: 2 +standardTime: 0.003000525987056609 generations: 54.64 N: 9,973 changeTypes: 1 +standardTime: 0.25170533192749617 generations: 5015.30 N: 113 changeTypes: 0 +maxLogL = -201.23329554404444 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 9,917 changeTypes: 1 +standardTime: 0.25302780051044 generations: 5018.46 N: 112 changeTypes: 0 +maxLogL = -201.45624462979086 + +computing time = 335.55 seconds diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..5a9009ec7fd14d964a955ab1d85863ebc4511329 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 9917 +5018 9917 +5018 112 +4000000 112 + diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/receipt_51935444.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/receipt_51935444.json new file mode 100644 index 0000000000000000000000000000000000000000..e1ed47a81f4420492a774697c148e8cac529af5e --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/receipt_51935444.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "d14f716d0aaaaa4c6f9dc2ef74b477b98584057c3c26f43a1040147cea8e8b6b", + "elapsed_s": 355, + "failure_sha256": null, + "host": "cn605-21-l", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935444", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "7264cadf47259c94cdc61654b71ab2812166068a22d277b4193d6e12880f62b9", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:06:27Z" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..863be47d6feca3508852e8212733e9b40084bca0 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g1/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g1/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X100_5K/receipts/export_51933438.json"], "job_id": "51935444", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X100_5K/fitcoal_g1.json", "request_sha256": "d43ab19a3c1264894d20dea6085ed021746567bf5f51639d3f6570075e56020a", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [1], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "7264cadf47259c94cdc61654b71ab2812166068a22d277b4193d6e12880f62b9", "stage": "v2", "usage_before": {"account_jobs": 187, "bench_cores": 575, "bench_gpus": 19, "bench_jobs": 116, "bench_pending": 83, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:36:19Z"} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/envlock_check_51935538.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/envlock_check_51935538.json new file mode 100644 index 0000000000000000000000000000000000000000..f0f06e649ab36257918a86e215beed4a4a65d878 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/envlock_check_51935538.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn504-03", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935538", + "status": "PASS", + "utc": "20260916T120305Z" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..aee927633e829d23ef453798050ad01ebb2fd022 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X100_5K", + "g": 2, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X100_5K/r00000002/n32" + ], + "rep": 2, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..15c76e3b9bab6e4852458b843c334465e77b7891 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +13046 5884 3568 2323 1870 1348 1030 842 680 484 427 344 258 203 191 140 127 114 82 88 62 50 52 38 32 24 19 26 13 13 6 14 15 6 13 9 2 4 8 4 2 4 6 6 3 2 2 5 3 4 2 4 6 1 1 2 1 2 4 2 1 2 2 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..d0834d239fece68b6fbf4afe90e1abbc4ef974ab --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g2/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g2/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 2 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..8b86285c58b6f3f9a0d45993eff6aabc1f783341 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 4,727 changeTypes: 0 +maxLogL = -10779.39421944577 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 9,728 changeTypes: 1 +standardTime: 0.2598206444563435 generations: 5055.15 N: 97 changeTypes: 0 +maxLogL = -200.72781968583533 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 9,375 changeTypes: 1 +standardTime: 0.0828259228235138 generations: 1552.96 N: 10,957 changeTypes: 1 +standardTime: 0.24109669524484212 generations: 5021.15 N: 110 changeTypes: 0 +maxLogL = -194.78790291489858 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 9,728 changeTypes: 1 +standardTime: 0.2598206444563435 generations: 5055.15 N: 97 changeTypes: 0 +maxLogL = -200.72781968583533 + +computing time = 163.54 seconds diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..b1e1bed2c0dcf5b5bceb3e80f53ff7793e95282b --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 9728 +5055 9728 +5055 97 +4000000 97 + diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/receipt_51935538.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/receipt_51935538.json new file mode 100644 index 0000000000000000000000000000000000000000..414df6a71582c0fb0dc263949916c8acbbd61bac --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/receipt_51935538.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "df08ddb50d48ee8c84ec66220f45d57d6fa776f02639ae8fa781cca5f9a868f8", + "elapsed_s": 188, + "failure_sha256": null, + "host": "cn504-03", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935538", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "c1b090b8d00d07e055edd6ed8525ce222ce6b7d3a846386429163c9d6230f963", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:05:56Z" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..c26d0a3f2678ddaa45953c330fcd6b0fbec26178 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g2/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g2/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X100_5K/receipts/export_51933438.json"], "job_id": "51935538", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X100_5K/fitcoal_g2.json", "request_sha256": "ad57210e291f819ee15600ca5636aa91b42d692deda09991b20d4b9f6711f05a", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [2], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "c1b090b8d00d07e055edd6ed8525ce222ce6b7d3a846386429163c9d6230f963", "stage": "v2", "usage_before": {"account_jobs": 212, "bench_cores": 638, "bench_gpus": 19, "bench_jobs": 141, "bench_pending": 115, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:40:02Z"} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/envlock_check_51935540.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/envlock_check_51935540.json new file mode 100644 index 0000000000000000000000000000000000000000..ee9d5efe6a7c3b34d198e6cc8d1d7fe4125f49dd --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/envlock_check_51935540.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn504-02", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935540", + "status": "PASS", + "utc": "20260916T120256Z" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..f54997b0a9a3e431455228bca583548048361c13 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X100_5K", + "g": 3, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X100_5K/r00000003/n32" + ], + "rep": 3, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..4abe4ced6050bfcd359dc808089dbc537b0b2889 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +13586 6082 3659 2478 1654 1292 1001 753 617 546 445 291 245 204 161 129 132 116 79 76 63 56 37 35 31 28 22 35 26 16 10 7 7 8 6 4 9 8 5 4 7 6 6 2 5 5 1 2 2 5 4 4 2 1 1 3 2 5 2 1 3 2 3 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..235e8f566b6d7ebecf28eedbb028ced1e3eb18bf --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g3/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g3/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 1 -randSeed 3 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..c2cae29985b9984ee8a1cd6e33a807d04ed6d7f0 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 4,815 changeTypes: 0 +maxLogL = -11200.921561177212 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 10,094 changeTypes: 1 +standardTime: 0.24627066713250542 generations: 4971.57 N: 101 changeTypes: 0 +maxLogL = -193.66219613320973 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 10,112 changeTypes: 1 +standardTime: 0.24356432663315317 generations: 4925.64 N: 162 changeTypes: 1 +standardTime: 1.027008510707184 generations: 5180.15 N: 74 changeTypes: 0 +maxLogL = -193.43625038582775 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 10,094 changeTypes: 1 +standardTime: 0.24627066713250542 generations: 4971.57 N: 101 changeTypes: 0 +maxLogL = -193.66219613320973 + +computing time = 184.79 seconds diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..4d139e4bc712412628018f645c578108cc74aa53 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 10094 +4972 10094 +4972 101 +4000000 101 + diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..5dc872fd79c57a0630616d4dc65b24263eb0d126 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 1 (recommended) +The proportion of truncated or collapsed SFS types: 0.015873015873015872 + diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/receipt_51935540.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/receipt_51935540.json new file mode 100644 index 0000000000000000000000000000000000000000..5969ef25f2f724744b62ab8fd86fcb9ec8e5be02 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/receipt_51935540.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "2d3accfc1f2dc159f1d0f35e50ec3891da304215774d579866150aac20fdf746", + "elapsed_s": 201, + "failure_sha256": null, + "host": "cn504-02", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935540", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "e4c2c21a4f33ba6b33bda4b14064393bb3439905e7507d91178f84d0a2db129b", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:06:09Z" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..4b23257bba30bb18581b43825467707b1e66e64b --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g3/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g3/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X100_5K/receipts/export_51933438.json"], "job_id": "51935540", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X100_5K/fitcoal_g3.json", "request_sha256": "c53d73ed1d52480d1bec9ebcbb9c9dcdb37457f9a7fe2be6f2a7f7363d224f71", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [3], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "e4c2c21a4f33ba6b33bda4b14064393bb3439905e7507d91178f84d0a2db129b", "stage": "v2", "usage_before": {"account_jobs": 213, "bench_cores": 640, "bench_gpus": 19, "bench_jobs": 142, "bench_pending": 116, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:40:06Z"} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/envlock_check_51935542.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/envlock_check_51935542.json new file mode 100644 index 0000000000000000000000000000000000000000..ec16d17aab926ef67f59e052b1afe321677db4da --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/envlock_check_51935542.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn504-02", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935542", + "status": "PASS", + "utc": "20260916T120250Z" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..172103ce8f7e9ab9b530a2efe0f2047b7a6077e2 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X100_5K", + "g": 4, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X100_5K/r00000004/n32" + ], + "rep": 4, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..7c722e51b49ed2a5cae1f85b286e11ced3ee6325 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +13189 6171 3447 2388 1652 1295 950 782 615 498 398 305 281 227 204 150 126 117 108 76 73 50 50 33 29 31 25 24 25 19 7 15 11 7 7 8 6 8 9 6 4 4 2 5 5 3 5 1 3 3 3 4 1 2 4 3 4 4 3 5 4 2 3 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..2f83fc5628a33755402edd89783278ae4ab495e6 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g4/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g4/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 4 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..4120b724c3c096054f645c721b14dadff7f46381 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 4,723 changeTypes: 0 +maxLogL = -10784.397295539688 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 9,786 changeTypes: 1 +standardTime: 0.25466010087628926 generations: 4984.37 N: 110 changeTypes: 0 +maxLogL = -188.61471882362957 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 9,974 changeTypes: 2 +standardTime: 0.1462265011005797 generations: 2837.87 N: 9,443 changeTypes: 1 +standardTime: 0.2604787323595295 generations: 4995.74 N: 106 changeTypes: 0 +maxLogL = -188.03479478193 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 9,786 changeTypes: 1 +standardTime: 0.25466010087628926 generations: 4984.37 N: 110 changeTypes: 0 +maxLogL = -188.61471882362957 + +computing time = 173.50 seconds diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..34bc22998fffd60cfc8f4620f6f42b1806cc3b3a --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 9786 +4984 9786 +4984 110 +4000000 110 + diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/receipt_51935542.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/receipt_51935542.json new file mode 100644 index 0000000000000000000000000000000000000000..4129da171daf0ab5212b29cb7f130d8d302f0c0b --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/receipt_51935542.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "0bc8cf1b3e0a941516ec765ee04f83a3e9eaee352feb0369bbd7f8aa4d280303", + "elapsed_s": 186, + "failure_sha256": null, + "host": "cn504-02", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935542", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "567f0feb96dde022c7820d3f2080b999c3e2d2858bbdc3d1e2857769b3b781e4", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:05:54Z" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..95c250d355f61472bd77995f1e9a339725a18282 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g4/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g4/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X100_5K/receipts/export_51933438.json"], "job_id": "51935542", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X100_5K/fitcoal_g4.json", "request_sha256": "ede972b7f764fef00579324e3eff429a7b062eb6bd120b110a5659fc28d7c7b3", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [4], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "567f0feb96dde022c7820d3f2080b999c3e2d2858bbdc3d1e2857769b3b781e4", "stage": "v2", "usage_before": {"account_jobs": 214, "bench_cores": 642, "bench_gpus": 19, "bench_jobs": 143, "bench_pending": 117, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:40:10Z"} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/envlock_check_51935544.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/envlock_check_51935544.json new file mode 100644 index 0000000000000000000000000000000000000000..7bb1beb4ed145c12085bc7e47a8dc30b5ed84a8e --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/envlock_check_51935544.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn605-21-l", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935544", + "status": "PASS", + "utc": "20260916T121142Z" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..515fad9a145ddb3670609a444c647418d66ae517 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X100_5K", + "g": 5, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X100_5K/r00000005/n32" + ], + "rep": 5, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..b05dfcdd76ef5bbe1d904da05d306107ba204a60 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +13090 5869 3801 2435 1771 1287 978 737 563 463 382 327 244 196 181 164 118 100 84 62 55 52 51 43 35 24 33 22 18 16 12 11 9 13 8 4 8 12 10 1 4 3 4 3 6 4 3 4 0 6 2 0 2 2 1 1 1 0 2 3 2 0 2 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..7742a196ca31a34b79e930617b8c6cf2ec26adaa --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g5/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g5/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 5 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..c33ce345dfe77b7330e153c5dc6a73c6ff880762 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 4,701 changeTypes: 0 +maxLogL = -11024.179376623857 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 9,832 changeTypes: 1 +standardTime: 0.24974052188118043 generations: 4910.89 N: 98 changeTypes: 0 +maxLogL = -199.06056513820982 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 9,880 changeTypes: 1 +standardTime: 0.24207877145382573 generations: 4783.56 N: 285 changeTypes: 1 +standardTime: 0.9984241114630211 generations: 5214.14 N: 11 changeTypes: 0 +maxLogL = -195.55541551632646 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 9,832 changeTypes: 1 +standardTime: 0.24974052188118043 generations: 4910.89 N: 98 changeTypes: 0 +maxLogL = -199.06056513820982 + +computing time = 361.29 seconds diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..6d4fac115a00a49a1b1893b8948ea6ef22fda606 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 9832 +4911 9832 +4911 98 +4000000 98 + diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/receipt_51935544.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/receipt_51935544.json new file mode 100644 index 0000000000000000000000000000000000000000..3e9ab19af14eeed01934c9b19250b64b575c26d7 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/receipt_51935544.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "bda32345760e80e21f38e1970dc23d9fba9237be44ad9dd8507c29a3559bbdaf", + "elapsed_s": 910, + "failure_sha256": null, + "host": "cn605-21-l", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935544", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "e90601f0abe4d185336bfef84861cad0003001278f440388cf87d45a65e33440", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:17:58Z" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..e6a8c30003be1b21a3aeb536ef68616356ae5b85 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g5/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g5/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X100_5K/receipts/export_51933438.json"], "job_id": "51935544", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X100_5K/fitcoal_g5.json", "request_sha256": "02aa0691d403b7b8b291f5bc92802fe6f8adf2db1e46b0c2eaaf1ba97dc35119", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [5], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "e90601f0abe4d185336bfef84861cad0003001278f440388cf87d45a65e33440", "stage": "v2", "usage_before": {"account_jobs": 215, "bench_cores": 644, "bench_gpus": 19, "bench_jobs": 144, "bench_pending": 118, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:40:14Z"} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/envlock_check_51935545.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/envlock_check_51935545.json new file mode 100644 index 0000000000000000000000000000000000000000..c22351b24ddb0f83516f2d6585f3541fd5270cd1 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/envlock_check_51935545.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn605-21-l", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935545", + "status": "PASS", + "utc": "20260916T121106Z" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..3be1e1743b915d677f1a8672173547a0d70fbbd3 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X100_5K", + "g": 6, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X100_5K/r00000006/n32" + ], + "rep": 6, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..1e0b6c970e644f4f6b34ec3be29403dce27f568e --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +13598 5888 3455 2613 1660 1301 1084 759 584 502 410 329 293 232 200 156 141 99 97 87 72 61 57 37 25 27 23 35 25 19 8 25 23 20 13 9 7 5 8 5 7 4 3 8 6 7 6 5 2 8 2 6 5 1 4 3 15 5 5 3 2 13 2 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..28319935b2f6bb09547ccfe41565e7bdc7de2630 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g6/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g6/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 2 -randSeed 6 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..73a467075948911e36ae0317057dcd0232915467 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 4,841 changeTypes: 0 +maxLogL = -10492.461641654872 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 9,928 changeTypes: 1 +standardTime: 0.25305422686865053 generations: 5024.42 N: 169 changeTypes: 0 +maxLogL = -223.04225183303737 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 23,204 changeTypes: 2 +standardTime: 0.001959241682965602 generations: 57.03 N: 9,720 changeTypes: 1 +standardTime: 0.25838102302693855 generations: 5041.78 N: 162 changeTypes: 0 +maxLogL = -220.0234230805492 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 9,928 changeTypes: 1 +standardTime: 0.25305422686865053 generations: 5024.42 N: 169 changeTypes: 0 +maxLogL = -223.04225183303737 + +computing time = 342.79 seconds diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..0dd969e31f0b3e5c039d60bcc56eb48aa3ff1aed --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 9928 +5024 9928 +5024 169 +4000000 169 + diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..a58943a48f97b8f2d3333cf34f4a28b685cf1127 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 2 (recommended) +The proportion of truncated or collapsed SFS types: 0.031746031746031744 + diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/receipt_51935545.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/receipt_51935545.json new file mode 100644 index 0000000000000000000000000000000000000000..6406ddc3ee228cb27b4652efe8b8f454d417bde1 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/receipt_51935545.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "e873be2d9ffaa1a5a071dc02178c4ce3d7488fc2c1913cea307d09952683c728", + "elapsed_s": 862, + "failure_sha256": null, + "host": "cn605-21-l", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935545", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "60f81cd5891e00439bf89c71ed3e9fb10961fb250fba943760d2ab1e98057258", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:17:10Z" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..f8b1fad7794f579a8f23a1f9e19b82005c666fc9 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g6/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g6/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X100_5K/receipts/export_51933438.json"], "job_id": "51935545", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X100_5K/fitcoal_g6.json", "request_sha256": "e886e30a32578f1f144e4de181a8838143fe811c61a3e837e31f8a179189600f", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [6], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "60f81cd5891e00439bf89c71ed3e9fb10961fb250fba943760d2ab1e98057258", "stage": "v2", "usage_before": {"account_jobs": 216, "bench_cores": 646, "bench_gpus": 19, "bench_jobs": 145, "bench_pending": 119, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:40:18Z"} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/envlock_check_51935546.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/envlock_check_51935546.json new file mode 100644 index 0000000000000000000000000000000000000000..9a5777022d93acefc9034225789d439ba5836f4a --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/envlock_check_51935546.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn605-19-r", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935546", + "status": "PASS", + "utc": "20260916T121211Z" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..e9461e155b3c39200b4328283386714a99237f2f --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X100_5K", + "g": 7, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X100_5K/r00000007/n32" + ], + "rep": 7, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6b74f925ee491b90a4a796d991fa4d9f7f04d1e --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +13981 6021 3475 2269 1829 1337 955 753 622 511 398 291 258 230 174 167 138 102 106 80 64 55 38 53 53 39 42 16 20 16 24 21 13 13 12 13 11 19 21 9 8 5 11 8 20 6 9 4 6 7 3 9 2 5 4 5 6 3 6 2 6 5 3 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..b630439913d8e1cb3873b103fad0f2b7dcbc1ea6 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g7/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g7/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 7 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..cf61cbcd0e80f9313448ab5dbf7ae2b37e4886e8 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 4,849 changeTypes: 0 +maxLogL = -10787.446763334025 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 10,167 changeTypes: 1 +standardTime: 0.239090384378331 generations: 4861.82 N: 239 changeTypes: 0 +maxLogL = -232.9255853088366 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 13,313 changeTypes: 2 +standardTime: 0.015507147421787307 generations: 350.25 N: 9,662 changeTypes: 1 +standardTime: 0.251435613048375 generations: 4909.37 N: 223 changeTypes: 0 +maxLogL = -223.0087520446997 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 10,167 changeTypes: 1 +standardTime: 0.239090384378331 generations: 4861.82 N: 239 changeTypes: 0 +maxLogL = -232.9255853088366 + +computing time = 386.14 seconds diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..496d727fce585273776cff1c546028afccfeed56 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 10167 +4862 10167 +4862 239 +4000000 239 + diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/receipt_51935546.json b/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/receipt_51935546.json new file mode 100644 index 0000000000000000000000000000000000000000..110fbdd90085928ffccc952aa4f7aa0270befd0f --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/receipt_51935546.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "6fa2bb0059b17a213ab7601ac06fd536e3124b90c0b1072a188e3493127df743", + "elapsed_s": 967, + "failure_sha256": null, + "host": "cn605-19-r", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935546", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "f92ddd396b9af1ba5ad6476a8d3bca89c28bcd9613d9a0c10d476565f852b4c1", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:18:55Z" +} diff --git a/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..77aca4357aea08a7d7e4f91e21a1dbcce1de8b96 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X100_5K/K1/g7/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X100_5K/K1/g7/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X100_5K/receipts/export_51933438.json"], "job_id": "51935546", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X100_5K/fitcoal_g7.json", "request_sha256": "12dd6fe5e60796e406d2d0625ab6a9a83ed8ab63b341272918a606cfcfd82937", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [7], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "f92ddd396b9af1ba5ad6476a8d3bca89c28bcd9613d9a0c10d476565f852b4c1", "stage": "v2", "usage_before": {"account_jobs": 216, "bench_cores": 646, "bench_gpus": 19, "bench_jobs": 145, "bench_pending": 120, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:40:22Z"} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/envlock_check_51935132.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/envlock_check_51935132.json new file mode 100644 index 0000000000000000000000000000000000000000..bd10dae5ecc7eb4902974e77af1dad35551b9e5a --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/envlock_check_51935132.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-11", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935132", + "status": "PASS", + "utc": "20260916T115340Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..9927cf8e5796f9a8a452e3137221aa219d7ddea6 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X10_1K", + "g": 0, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_1K/r00000000/n32" + ], + "rep": 0, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..322f5e5ef19dacd1ef17c99edddff67954a3f619 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +11271 4759 2912 2356 1956 1587 1478 1336 1336 1273 1247 1137 991 910 960 846 837 785 722 799 689 736 681 655 587 610 627 537 462 488 480 458 442 426 412 392 439 396 382 404 377 365 357 351 328 324 319 319 333 314 292 280 315 278 348 280 286 303 279 267 152 167 222 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..c35f56250b57bf9c73a5b1fef9141d43be2580e8 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g0/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g0/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 3 -randSeed 0 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..96c22909a05dbcdd7d9a7be02b2b288df4aabb6a --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 7,994 changeTypes: 0 +maxLogL = -1365.695760255692 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 6,461 changeTypes: 1 +standardTime: 0.6113805992741933 generations: 7900.32 N: 11,075 changeTypes: 0 +maxLogL = -537.6187808352995 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 10,131 changeTypes: 1 +standardTime: 0.04264717656081746 generations: 864.14 N: 738 changeTypes: 2 +standardTime: 0.21589799827544187 generations: 1590.01 N: 10,298 changeTypes: 0 +maxLogL = -303.35629178414547 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 10,152 changeTypes: 1 +standardTime: 0.04423669717974967 generations: 898.14 N: 126 changeTypes: 1 +standardTime: 0.16406644890894487 generations: 928.26 N: 9,674 changeTypes: 1 +standardTime: 1.6780558287767358 generations: 30221.88 N: 11,564 changeTypes: 0 +maxLogL = -301.0883921592945 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 10,131 changeTypes: 1 +standardTime: 0.04264717656081746 generations: 864.14 N: 738 changeTypes: 2 +standardTime: 0.21589799827544187 generations: 1590.01 N: 10,298 changeTypes: 0 +maxLogL = -303.35629178414547 + +computing time = 770.73 seconds diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..fd753206b26b9218c64b03f6f938462ff07b068f --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 10298 +4000000 10298 + diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..47de88aebecef4006ba97a94faaf20de764f8f92 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 3 (recommended) +The proportion of truncated or collapsed SFS types: 0.047619047619047616 + diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/receipt_51935132.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/receipt_51935132.json new file mode 100644 index 0000000000000000000000000000000000000000..6ad1420137c05d5db4ecaddf1cfe86b6873a6c93 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/receipt_51935132.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "8a755a0a8c188e84f76f707eb375414d428aebd88c19f0a6f52a7a5d7f5a92e7", + "elapsed_s": 787, + "failure_sha256": null, + "host": "cn604-11", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935132", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "8f87eafd55b5262bf60fcc2a5c720eb0ce9b331598cfcbcf399cef6f48f80714", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:06:46Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..13b64f2b193183e0591d3344adc708c13e20a4f4 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g0/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g0/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_1K/receipts/export_51933154.json"], "job_id": "51935132", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X10_1K/fitcoal_g0.json", "request_sha256": "f46144575cc3cf4c7eb8df265e2de8ee0746001e089a7492cb265d95fa5a0242", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [0], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "8f87eafd55b5262bf60fcc2a5c720eb0ce9b331598cfcbcf399cef6f48f80714", "stage": "v2", "usage_before": {"account_jobs": 163, "bench_cores": 443, "bench_gpus": 19, "bench_jobs": 92, "bench_pending": 24, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:32:17Z"} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/envlock_check_51935140.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/envlock_check_51935140.json new file mode 100644 index 0000000000000000000000000000000000000000..18327686e1ab44caab1f2fe0f5e6d36f1778a38a --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/envlock_check_51935140.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-11", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935140", + "status": "PASS", + "utc": "20260916T115340Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..e6ec14be580d464860e72e26cf6c16832daaa0e9 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X10_1K", + "g": 1, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_1K/r00000001/n32" + ], + "rep": 1, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..f82f50cf4d132687887135813262dfe4d498d7a1 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +12137 5166 3148 2370 1799 1657 1467 1460 1225 1198 1033 937 976 940 1007 896 829 768 758 785 752 640 650 591 603 604 596 545 470 498 475 494 465 442 357 391 431 408 395 400 395 348 362 367 370 307 327 336 343 280 304 269 305 305 278 268 214 252 237 259 265 243 237 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..28ee6fb6fba2531175634169f6792eac0747f995 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g1/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g1/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 1 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..ea86674c18bdfd14df6c887009fcbe92293fc511 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 8,126 changeTypes: 0 +maxLogL = -1177.1127195317986 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 6,935 changeTypes: 1 +standardTime: 0.72823215219179 generations: 10099.91 N: 10,914 changeTypes: 0 +maxLogL = -620.8270526571213 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 10,373 changeTypes: 1 +standardTime: 0.05738479486442658 generations: 1190.49 N: 243 changeTypes: 1 +standardTime: 0.20350308001535522 generations: 1261.40 N: 10,183 changeTypes: 0 +maxLogL = -320.00381149044085 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 10,325 changeTypes: 1 +standardTime: 0.05801729196756863 generations: 1198.05 N: 448 changeTypes: 1 +standardTime: 0.21748244910779505 generations: 1341.05 N: 10,520 changeTypes: 1 +standardTime: 1.9941924470553247 generations: 38722.98 N: 9,201 changeTypes: 0 +maxLogL = -319.54739075643226 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 10,373 changeTypes: 1 +standardTime: 0.05738479486442658 generations: 1190.49 N: 243 changeTypes: 1 +standardTime: 0.20350308001535522 generations: 1261.40 N: 10,183 changeTypes: 0 +maxLogL = -320.00381149044085 + +computing time = 826.07 seconds diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..56e1a452a6b9dbf515dca5be667a23459e53cdf1 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 10183 +4000000 10183 + diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/receipt_51935140.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/receipt_51935140.json new file mode 100644 index 0000000000000000000000000000000000000000..c1eb5c98bf0f00a087e6b9e271adc12d1f5b0423 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/receipt_51935140.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "58ca34e4db6c7947ed359a5f24ae6b5c8e8511cd7a16abaa93961b6dc1c7375a", + "elapsed_s": 842, + "failure_sha256": null, + "host": "cn604-11", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935140", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "eb6a992402971f3011c0a5fd5257854fa9222a0b029e59d56aa1fd590888fd2c", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:07:41Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..a7644df47222fbb8417161ae41a93a7e57e6cb1f --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g1/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g1/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_1K/receipts/export_51933154.json"], "job_id": "51935140", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X10_1K/fitcoal_g1.json", "request_sha256": "96fbfb3921e31f08a486921ae6a81d3ccb2d7d13d28e76b9db078638d3e1cf1a", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [1], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "eb6a992402971f3011c0a5fd5257854fa9222a0b029e59d56aa1fd590888fd2c", "stage": "v2", "usage_before": {"account_jobs": 164, "bench_cores": 445, "bench_gpus": 19, "bench_jobs": 93, "bench_pending": 25, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:32:21Z"} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/envlock_check_51935142.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/envlock_check_51935142.json new file mode 100644 index 0000000000000000000000000000000000000000..abdc6586671b458841ed7b19da496354a0cac5d3 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/envlock_check_51935142.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-11", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935142", + "status": "PASS", + "utc": "20260916T115340Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..dbe7b62d346b19b2769d8823cc5254e48c71987f --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X10_1K", + "g": 2, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_1K/r00000002/n32" + ], + "rep": 2, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..f1914d1b2121a76b77fb15fee06ecdff10a6ffd6 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +11830 5141 3190 2316 1991 1698 1553 1340 1243 1108 1037 1072 1005 943 880 883 884 877 724 753 760 700 631 714 577 642 559 592 550 515 502 485 492 488 407 419 403 432 370 425 348 410 337 314 312 355 330 349 291 251 279 254 253 276 200 232 294 226 282 256 288 240 264 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..83b08e5c562385331fec477a15c5ef51bfa8dddf --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g2/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g2/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 2 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..332437a04ac29751d52f56082a3d42feb22b6708 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 8,146 changeTypes: 0 +maxLogL = -1212.1688543162536 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 6,817 changeTypes: 1 +standardTime: 0.5954941503021608 generations: 8118.92 N: 10,671 changeTypes: 0 +maxLogL = -601.2734457085514 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 9,768 changeTypes: 1 +standardTime: 0.06215309116545979 generations: 1214.28 N: 239 changeTypes: 1 +standardTime: 0.20425541553215606 generations: 1282.33 N: 10,279 changeTypes: 0 +maxLogL = -345.4903730872196 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 9,549 changeTypes: 1 +standardTime: 0.06605084554859053 generations: 1261.40 N: 1,289 changeTypes: 1 +standardTime: 0.3992901462602506 generations: 2120.32 N: 78,621 changeTypes: 1 +standardTime: 0.4351583213934804 generations: 7760.32 N: 9,631 changeTypes: 0 +maxLogL = -334.42012271752026 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 9,768 changeTypes: 1 +standardTime: 0.06215309116545979 generations: 1214.28 N: 239 changeTypes: 1 +standardTime: 0.20425541553215606 generations: 1282.33 N: 10,279 changeTypes: 0 +maxLogL = -345.4903730872196 + +computing time = 837.31 seconds diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f9e0595c91bd979f63daab79b729ad4e73cff8e --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 10279 +4000000 10279 + diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/receipt_51935142.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/receipt_51935142.json new file mode 100644 index 0000000000000000000000000000000000000000..5f03ee27799570e6cb2b518150d81f95b618b479 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/receipt_51935142.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "95447dae15d745f45f6da252756c63d29e26493f78b198d351f626c9b6db1f35", + "elapsed_s": 853, + "failure_sha256": null, + "host": "cn604-11", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935142", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "079a9500e65edeca81d1126cf78696a7d251467d1a0e6b414af51afbcbd1bb94", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:07:52Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..1d113393ef351e84038977f2d7d2ccddabf27d0d --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g2/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g2/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_1K/receipts/export_51933154.json"], "job_id": "51935142", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X10_1K/fitcoal_g2.json", "request_sha256": "1c1f0e964240239a8154f58a73748b31fb80e535a67982da88acf65d9d239d86", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [2], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "079a9500e65edeca81d1126cf78696a7d251467d1a0e6b414af51afbcbd1bb94", "stage": "v2", "usage_before": {"account_jobs": 163, "bench_cores": 445, "bench_gpus": 19, "bench_jobs": 92, "bench_pending": 26, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:32:27Z"} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/envlock_check_51935160.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/envlock_check_51935160.json new file mode 100644 index 0000000000000000000000000000000000000000..927b828b1cd76533f90f796623f4c0d405fb1136 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/envlock_check_51935160.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-11", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935160", + "status": "PASS", + "utc": "20260916T115340Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..40cc5b6e4ccd0fe958be60f302def722d86ee669 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X10_1K", + "g": 3, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_1K/r00000003/n32" + ], + "rep": 3, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..9fc79011e59dfd68f38316252257d3e06487a602 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +11581 4900 3022 2040 1810 1560 1523 1306 1145 1192 1060 972 936 967 906 893 922 830 785 740 701 711 654 630 666 624 581 504 533 565 571 468 486 447 483 436 405 456 414 355 342 326 331 375 311 309 324 298 268 317 277 294 238 271 216 244 279 228 250 235 281 241 242 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..dd56bd66888e4ecb0c0276f7102fec57735f7d09 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g3/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g3/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 3 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..7a6b18f099c4cd927a68ab956e5a16a9db34d9c7 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 7,935 changeTypes: 0 +maxLogL = -1453.272734650594 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 6,486 changeTypes: 1 +standardTime: 0.5826706276729195 generations: 7558.11 N: 10,631 changeTypes: 0 +maxLogL = -716.846041351666 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 10,302 changeTypes: 1 +standardTime: 0.05145373715113467 generations: 1060.11 N: 170 changeTypes: 1 +standardTime: 0.20932263276564184 generations: 1113.89 N: 10,262 changeTypes: 0 +maxLogL = -343.011078484398 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 10,033 changeTypes: 1 +standardTime: 0.05455441022778377 generations: 1094.72 N: 1,042 changeTypes: 1 +standardTime: 0.3922958754076043 generations: 1798.85 N: 32,254 changeTypes: 1 +standardTime: 0.5179046215475052 generations: 9901.52 N: 9,297 changeTypes: 0 +maxLogL = -323.47597722765283 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 10,302 changeTypes: 1 +standardTime: 0.05145373715113467 generations: 1060.11 N: 170 changeTypes: 1 +standardTime: 0.20932263276564184 generations: 1113.89 N: 10,262 changeTypes: 0 +maxLogL = -343.011078484398 + +computing time = 870.11 seconds diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..dede6a5512ca6709ad4d5c923f11b72f2a25b3a5 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 10262 +4000000 10262 + diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/receipt_51935160.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/receipt_51935160.json new file mode 100644 index 0000000000000000000000000000000000000000..9077d9fce7a98bf9d272c817a951d74f5bcc1cd8 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/receipt_51935160.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "b9d3cf440ff495cbcece675e3f220188b945b6ca3aed05dff7b59d3ff76a7057", + "elapsed_s": 886, + "failure_sha256": null, + "host": "cn604-11", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935160", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "5957bf9a8fb36c1f0be27b154818d6e84e0c597a7e3073d2bf6a0acae2d55a39", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:08:25Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..52b0b8ec41cdce241a5f6fda7eff20f320c40035 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g3/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g3/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_1K/receipts/export_51933154.json"], "job_id": "51935160", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X10_1K/fitcoal_g3.json", "request_sha256": "2745cbe81e83a8ba6eae2e898c56b3140ad03a52e9e4b1f14bf127e67142ad06", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [3], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "5957bf9a8fb36c1f0be27b154818d6e84e0c597a7e3073d2bf6a0acae2d55a39", "stage": "v2", "usage_before": {"account_jobs": 162, "bench_cores": 445, "bench_gpus": 19, "bench_jobs": 91, "bench_pending": 27, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:32:33Z"} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/envlock_check_51935161.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/envlock_check_51935161.json new file mode 100644 index 0000000000000000000000000000000000000000..7f82644cc34a3675d2dc3b0a3a0ff94882102fd4 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/envlock_check_51935161.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-11", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935161", + "status": "PASS", + "utc": "20260916T115340Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..8e0e3e05ad4cc2783956aa23ca26eecccb87623e --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X10_1K", + "g": 4, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_1K/r00000004/n32" + ], + "rep": 4, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..9ba67374a498fa08ff0c41fdbf248a315ead7010 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +11688 4872 2775 2261 2088 1698 1389 1404 1305 1105 958 982 994 861 792 790 747 776 802 712 650 652 645 537 523 508 485 467 485 437 468 456 490 422 422 384 361 398 317 367 387 336 402 352 375 267 298 311 315 309 311 235 227 284 325 280 222 291 304 314 251 312 322 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..61d07677237916d670221f03d964fdaa947a5276 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g4/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g4/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 9 -randSeed 4 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..256acad3a7cd5712049600043386d90382d0bb6e --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 7,705 changeTypes: 0 +maxLogL = -989.5435880664776 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 6,723 changeTypes: 1 +standardTime: 0.945279902755743 generations: 12709.81 N: 11,204 changeTypes: 0 +maxLogL = -553.9612124043628 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 12,476 changeTypes: 1 +standardTime: 0.01970690807999458 generations: 491.71 N: 3,684 changeTypes: 2 +standardTime: 0.41770333602613274 generations: 5082.57 N: 9,769 changeTypes: 0 +maxLogL = -316.0174639407031 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 12,196 changeTypes: 1 +standardTime: 0.025837389277027514 generations: 630.23 N: 258 changeTypes: 1 +standardTime: 0.053139925294619555 generations: 644.31 N: 5,124 changeTypes: 1 +standardTime: 0.34631078541117155 generations: 3648.93 N: 9,786 changeTypes: 0 +maxLogL = -315.4640223109727 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 12,476 changeTypes: 1 +standardTime: 0.01970690807999458 generations: 491.71 N: 3,684 changeTypes: 2 +standardTime: 0.41770333602613274 generations: 5082.57 N: 9,769 changeTypes: 0 +maxLogL = -316.0174639407031 + +computing time = 817.01 seconds diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..0459679e3fbdd1bc8fc5d75135dbc167d0ad64fb --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fitcoal/output.txt @@ -0,0 +1,104 @@ +year popSize +2000 5075 +2031 5108 +2062 5142 +2092 5176 +2123 5210 +2154 5244 +2185 5278 +2216 5313 +2247 5348 +2277 5383 +2308 5419 +2339 5454 +2370 5490 +2401 5526 +2432 5562 +2462 5599 +2493 5636 +2524 5673 +2555 5710 +2586 5747 +2617 5785 +2647 5823 +2678 5862 +2709 5900 +2740 5939 +2771 5978 +2801 6017 +2832 6057 +2863 6096 +2894 6136 +2925 6177 +2956 6217 +2986 6258 +3017 6299 +3048 6341 +3079 6382 +3110 6424 +3141 6467 +3171 6509 +3202 6552 +3233 6595 +3264 6638 +3295 6682 +3326 6726 +3356 6770 +3387 6814 +3418 6859 +3449 6904 +3480 6950 +3510 6995 +3541 7041 +3572 7087 +3603 7134 +3634 7181 +3665 7228 +3695 7276 +3726 7323 +3757 7371 +3788 7420 +3819 7469 +3850 7518 +3880 7567 +3911 7617 +3942 7667 +3973 7717 +4004 7768 +4034 7819 +4065 7870 +4096 7922 +4127 7974 +4158 8027 +4189 8079 +4219 8132 +4250 8186 +4281 8240 +4312 8294 +4343 8348 +4374 8403 +4404 8458 +4435 8514 +4466 8570 +4497 8626 +4528 8683 +4559 8740 +4589 8797 +4620 8855 +4651 8913 +4682 8972 +4713 9031 +4743 9090 +4774 9150 +4805 9210 +4836 9270 +4867 9331 +4898 9393 +4928 9454 +4959 9516 +4990 9579 +5021 9642 +5052 9705 +5083 9769 +4000000 9769 + diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..015390263a90901dc3f7155b422a959bcbc7f873 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 9 (recommended) +The proportion of truncated or collapsed SFS types: 0.14285714285714285 + diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/receipt_51935161.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/receipt_51935161.json new file mode 100644 index 0000000000000000000000000000000000000000..6a7f463a90d5110a74977de80d88960ff03e22dd --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/receipt_51935161.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "71d8711c11e1d5f00f1500e6afa331ace62a3bf9eef7c792492cf03e6ae9816d", + "elapsed_s": 833, + "failure_sha256": null, + "host": "cn604-11", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935161", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "51338c3fb07aae5afca6bd66d1a8c79073452e98a1631f56ba2de9974fa5f23a", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:07:32Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..4941838e5f88c0b4046b93fef22d921bf6446b97 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g4/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g4/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_1K/receipts/export_51933154.json"], "job_id": "51935161", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X10_1K/fitcoal_g4.json", "request_sha256": "46c8921fa342235b1f81c93ffa015ebf8a48a68d6f7b03dc0e8b43119eb9fd8b", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [4], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "51338c3fb07aae5afca6bd66d1a8c79073452e98a1631f56ba2de9974fa5f23a", "stage": "v2", "usage_before": {"account_jobs": 159, "bench_cores": 435, "bench_gpus": 19, "bench_jobs": 88, "bench_pending": 28, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:32:36Z"} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/envlock_check_51935167.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/envlock_check_51935167.json new file mode 100644 index 0000000000000000000000000000000000000000..0469aa98bc7e37a954fab2bf75dc7aa5f99ef0f6 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/envlock_check_51935167.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-11", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935167", + "status": "PASS", + "utc": "20260916T115340Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..8c661e54bc33951756780b8fd58edf4edc541e70 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X10_1K", + "g": 5, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_1K/r00000005/n32" + ], + "rep": 5, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..51706849d2526bc0efc8b63fa93411cda18643ef --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +11324 4706 2883 2298 1860 1651 1579 1361 1294 1089 1114 1063 1074 869 855 720 744 691 748 654 618 626 496 542 475 498 569 560 467 497 453 472 445 405 462 381 442 358 351 371 311 347 330 255 301 354 298 300 319 289 308 309 288 238 276 266 333 320 231 237 211 270 241 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..b8e5b7cf5912477fe65f5afac110e3ad1aa43493 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g5/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g5/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 1 -randSeed 5 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..16f04f7ee82cc3dedfb5133d9e8581c5291723bc --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 7,704 changeTypes: 0 +maxLogL = -1107.145927078613 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 6,579 changeTypes: 1 +standardTime: 0.8270033170990386 generations: 10881.41 N: 10,774 changeTypes: 0 +maxLogL = -551.4908982195053 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 12,340 changeTypes: 1 +standardTime: 0.017028030183615258 generations: 420.24 N: 3,889 changeTypes: 2 +standardTime: 0.44541367955022393 generations: 5528.53 N: 9,811 changeTypes: 0 +maxLogL = -359.23017395596037 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 11,101 changeTypes: 1 +standardTime: 0.0328048377904426 generations: 728.30 N: 160 changeTypes: 1 +standardTime: 0.10492182052119212 generations: 751.42 N: 7,813 changeTypes: 1 +standardTime: 1.0777120589399833 generations: 15951.68 N: 10,856 changeTypes: 0 +maxLogL = -350.7975225738787 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 12,340 changeTypes: 1 +standardTime: 0.017028030183615258 generations: 420.24 N: 3,889 changeTypes: 2 +standardTime: 0.44541367955022393 generations: 5528.53 N: 9,811 changeTypes: 0 +maxLogL = -359.23017395596037 + +computing time = 818.09 seconds diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..50de791bf5f38ec3c7abc1dce711e1704ada8c42 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fitcoal/output.txt @@ -0,0 +1,104 @@ +year popSize +2000 5178 +2035 5211 +2071 5244 +2106 5278 +2141 5312 +2176 5346 +2212 5380 +2247 5415 +2282 5449 +2318 5484 +2353 5520 +2388 5555 +2423 5591 +2459 5626 +2494 5662 +2529 5699 +2565 5735 +2600 5772 +2635 5809 +2670 5846 +2706 5884 +2741 5922 +2776 5959 +2812 5998 +2847 6036 +2882 6075 +2917 6114 +2953 6153 +2988 6192 +3023 6232 +3059 6272 +3094 6312 +3129 6353 +3164 6394 +3200 6435 +3235 6476 +3270 6517 +3306 6559 +3341 6601 +3376 6643 +3411 6686 +3447 6729 +3482 6772 +3517 6815 +3553 6859 +3588 6903 +3623 6947 +3658 6992 +3694 7037 +3729 7082 +3764 7127 +3800 7173 +3835 7219 +3870 7265 +3905 7312 +3941 7359 +3976 7406 +4011 7453 +4047 7501 +4082 7549 +4117 7598 +4152 7646 +4188 7695 +4223 7745 +4258 7794 +4294 7844 +4329 7895 +4364 7945 +4399 7996 +4435 8047 +4470 8099 +4505 8151 +4541 8203 +4576 8256 +4611 8309 +4646 8362 +4682 8416 +4717 8470 +4752 8524 +4788 8579 +4823 8634 +4858 8689 +4893 8745 +4929 8801 +4964 8857 +4999 8914 +5035 8971 +5070 9029 +5105 9086 +5140 9145 +5176 9203 +5211 9262 +5246 9322 +5282 9382 +5317 9442 +5352 9502 +5387 9563 +5423 9624 +5458 9686 +5493 9748 +5529 9811 +4000000 9811 + diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..5dc872fd79c57a0630616d4dc65b24263eb0d126 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 1 (recommended) +The proportion of truncated or collapsed SFS types: 0.015873015873015872 + diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/receipt_51935167.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/receipt_51935167.json new file mode 100644 index 0000000000000000000000000000000000000000..94c56ff76b7912892a6be674b81e88d601a53c30 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/receipt_51935167.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "c011daa779f590b4fafe859bd4b86eaa5061d4292d57964008bdfe877a062b8c", + "elapsed_s": 834, + "failure_sha256": null, + "host": "cn604-11", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935167", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "cbe820c68794c302601d214dbe4ee6a1d6405d36def1fa130c36b3f403e0dd87", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:07:33Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..17a6d93e07d150fad79c4cb4d42c0d4374d08a2c --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g5/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g5/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_1K/receipts/export_51933154.json"], "job_id": "51935167", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X10_1K/fitcoal_g5.json", "request_sha256": "225358d07f73e73c1f80953a50b97241706f6539caa14988af0397fdaa66d922", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [5], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "cbe820c68794c302601d214dbe4ee6a1d6405d36def1fa130c36b3f403e0dd87", "stage": "v2", "usage_before": {"account_jobs": 159, "bench_cores": 435, "bench_gpus": 19, "bench_jobs": 88, "bench_pending": 29, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:32:40Z"} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/envlock_check_51935176.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/envlock_check_51935176.json new file mode 100644 index 0000000000000000000000000000000000000000..cd3341cc9300fc7bc8b433aaa730e590a1e1c6bf --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/envlock_check_51935176.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-02", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935176", + "status": "PASS", + "utc": "20260916T115625Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..8fb569b1129fecd53150f80fcc8d2502ed0de940 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X10_1K", + "g": 6, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_1K/r00000006/n32" + ], + "rep": 6, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..04713611d5dbc22ab51ce77ec1dc10f0442e7e1e --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +11144 4738 2754 2131 1806 1620 1586 1410 1291 1201 1003 1052 945 942 845 856 814 837 753 713 650 551 598 556 529 521 522 549 563 471 418 457 396 423 423 412 371 388 385 386 349 294 325 371 328 369 332 290 346 313 342 280 289 272 256 289 229 228 193 209 245 182 254 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..85abb0a4cdaee466a4267e5d89b39e8fa57a09e7 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g6/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g6/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 1 -randSeed 6 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..10d27337335a62ba908f13c3ec7179b0463dfd7d --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 7,688 changeTypes: 0 +maxLogL = -1229.3876942875067 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 6,368 changeTypes: 1 +standardTime: 0.5896049070417556 generations: 7508.76 N: 10,196 changeTypes: 0 +maxLogL = -598.5742310245447 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 10,725 changeTypes: 1 +standardTime: 0.03498411865815345 generations: 750.43 N: 1,049 changeTypes: 2 +standardTime: 0.21207638962501157 generations: 1674.52 N: 9,626 changeTypes: 0 +maxLogL = -340.388180375071 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 8,065 changeTypes: 2 +standardTime: 0.026173365242625125 generations: 709.90 N: 25,420 changeTypes: 2 +standardTime: 0.03850693887262454 generations: 765.50 N: 584 changeTypes: 2 +standardTime: 0.18607026801743842 generations: 1278.70 N: 9,582 changeTypes: 0 +maxLogL = -338.5066309287789 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 10,725 changeTypes: 1 +standardTime: 0.03498411865815345 generations: 750.43 N: 1,049 changeTypes: 2 +standardTime: 0.21207638962501157 generations: 1674.52 N: 9,626 changeTypes: 0 +maxLogL = -340.388180375071 + +computing time = 632.23 seconds diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..976fb979ac0cc81cd25146af014bbef9aecc7bd1 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 9626 +4000000 9626 + diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..5dc872fd79c57a0630616d4dc65b24263eb0d126 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 1 (recommended) +The proportion of truncated or collapsed SFS types: 0.015873015873015872 + diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/receipt_51935176.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/receipt_51935176.json new file mode 100644 index 0000000000000000000000000000000000000000..3caa448232e0c68413041e403a98f5760b463407 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/receipt_51935176.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "6895e8994bb1b26b2e837b671e2214e154093de7bc215343a1ea766f956f10c2", + "elapsed_s": 674, + "failure_sha256": null, + "host": "cn604-02", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935176", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "ded5b16b735afe8a512fcc81d777697eb17182295ce1b63d220fd7657909af24", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:07:11Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..3792c7217b10a3eef1b7fd89ce79b8bdf6a8bab8 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g6/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g6/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_1K/receipts/export_51933154.json"], "job_id": "51935176", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X10_1K/fitcoal_g6.json", "request_sha256": "46427fb20f8b339d8395322ca2631424552f5a5f9767ac6adecefd8308f74348", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [6], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "ded5b16b735afe8a512fcc81d777697eb17182295ce1b63d220fd7657909af24", "stage": "v2", "usage_before": {"account_jobs": 160, "bench_cores": 437, "bench_gpus": 19, "bench_jobs": 89, "bench_pending": 30, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:32:44Z"} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/envlock_check_51935183.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/envlock_check_51935183.json new file mode 100644 index 0000000000000000000000000000000000000000..6ee7f67a1492f5f00fc8cdad310e704bb6da0ef5 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/envlock_check_51935183.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-02", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935183", + "status": "PASS", + "utc": "20260916T115625Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..d18a15895cb3f7585d2649e61fe995133df2858c --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X10_1K", + "g": 7, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_1K/r00000007/n32" + ], + "rep": 7, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..a1f9895f838ba0158403bf34635415ce0dc1410a --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +11623 4954 3073 2179 1693 1600 1363 1236 1236 1153 994 984 1063 907 986 822 788 757 728 698 606 657 607 633 620 554 557 490 513 528 499 486 450 520 419 354 464 414 443 385 335 373 277 338 347 377 313 360 331 312 334 282 244 230 305 238 298 282 257 303 292 229 310 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..9323694cc9133a5720995ac33e5971f039ba678e --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g7/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g7/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 1 -randSeed 7 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..a6188a3154a96a4c34349ad3a023cbdaa709bf74 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 7,879 changeTypes: 0 +maxLogL = -1381.261132321214 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 6,603 changeTypes: 1 +standardTime: 0.8778127370272144 generations: 11591.99 N: 11,617 changeTypes: 0 +maxLogL = -659.9051753827732 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 9,916 changeTypes: 1 +standardTime: 0.05974454571960605 generations: 1184.87 N: 229 changeTypes: 2 +standardTime: 0.24360274235453047 generations: 1512.80 N: 10,270 changeTypes: 0 +maxLogL = -346.7397484818043 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 9,970 changeTypes: 1 +standardTime: 0.05863857252336739 generations: 1169.23 N: 180 changeTypes: 1 +standardTime: 0.21551526761401577 generations: 1225.67 N: 9,811 changeTypes: 1 +standardTime: 1.3739672920873849 generations: 23956.17 N: 10,785 changeTypes: 0 +maxLogL = -346.0571218403536 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 9,916 changeTypes: 1 +standardTime: 0.05974454571960605 generations: 1184.87 N: 229 changeTypes: 2 +standardTime: 0.24360274235453047 generations: 1512.80 N: 10,270 changeTypes: 0 +maxLogL = -346.7397484818043 + +computing time = 661.67 seconds diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..923cd20b54293b946a6b1c1467f6726647dc5bd8 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 10270 +4000000 10270 + diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..5dc872fd79c57a0630616d4dc65b24263eb0d126 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 1 (recommended) +The proportion of truncated or collapsed SFS types: 0.015873015873015872 + diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/receipt_51935183.json b/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/receipt_51935183.json new file mode 100644 index 0000000000000000000000000000000000000000..14e53850c0b085d9123fedb69eedb1734883ef64 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/receipt_51935183.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "21cbc92f19beb022f34c116499382cd290985327837d8d71d6b6b53a9c2eaab5", + "elapsed_s": 704, + "failure_sha256": null, + "host": "cn604-02", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935183", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "837e4d6556afe1b7ca6948cb18a9f1e5db12512a5eedc607e647fc2b5f86cfd0", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:07:41Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..058bf167ce5a07f3b46d3c4d4beec2f6f2a6140e --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_1K/K1/g7/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_1K/K1/g7/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_1K/receipts/export_51933154.json"], "job_id": "51935183", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X10_1K/fitcoal_g7.json", "request_sha256": "6b031762aaf7a3c878f9f90308e03aed8d8a24607b638bd92eaa5ca97abb3a41", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [7], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "837e4d6556afe1b7ca6948cb18a9f1e5db12512a5eedc607e647fc2b5f86cfd0", "stage": "v2", "usage_before": {"account_jobs": 160, "bench_cores": 437, "bench_gpus": 19, "bench_jobs": 89, "bench_pending": 31, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:32:48Z"} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/envlock_check_51935243.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/envlock_check_51935243.json new file mode 100644 index 0000000000000000000000000000000000000000..c074bc77b59bfefddf11efe1f98b239be92742a3 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/envlock_check_51935243.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn504-18", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935243", + "status": "PASS", + "utc": "20260916T115618Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..59450fe6fee4da128da25c05a6f7ac6733923dd6 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X10_5K", + "g": 0, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_5K/r00000000/n32" + ], + "rep": 0, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..ad0a21691ae48df3dcedb36a982a41c1e6044968 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +13787 6472 4330 2835 2149 1772 1382 1235 1029 860 782 691 616 538 580 480 479 454 444 396 329 335 366 350 384 336 328 299 289 273 244 283 235 260 252 283 266 282 273 251 291 245 219 268 266 241 215 241 220 233 281 221 241 211 245 230 286 211 215 192 227 238 221 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..85edf11f4c331fdf6bec4432c36f12268d257018 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g0/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g0/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 2 -randSeed 0 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..3bb912cff78dde328ca9208a4620adc91fc5d151 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 7,414 changeTypes: 0 +maxLogL = -1316.3107365801227 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 10,353 changeTypes: 1 +standardTime: 0.09518416010974282 generations: 1970.80 N: 6,152 changeTypes: 0 +maxLogL = -565.8303592477737 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 9,870 changeTypes: 1 +standardTime: 0.2870565722716662 generations: 5666.62 N: 944 changeTypes: 1 +standardTime: 1.2384536002644133 generations: 7462.56 N: 12,234 changeTypes: 0 +maxLogL = -302.7022709548336 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 9,257 changeTypes: 2 +standardTime: 0.11077849650904951 generations: 2334.59 N: 12,065 changeTypes: 2 +standardTime: 1.926126261040357 generations: 10074.71 N: 708 changeTypes: 2 +standardTime: 1.9989897577599138 generations: 10443.22 N: 22,552 changeTypes: 0 +maxLogL = -301.24227187631493 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 9,870 changeTypes: 1 +standardTime: 0.2870565722716662 generations: 5666.62 N: 944 changeTypes: 1 +standardTime: 1.2384536002644133 generations: 7462.56 N: 12,234 changeTypes: 0 +maxLogL = -302.7022709548336 + +computing time = 797.71 seconds diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..75b67c2d653051fbb0805255c5eed2d8ee6b9136 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fitcoal/output.txt @@ -0,0 +1,8 @@ +year popSize +2000 9870 +5667 9870 +5667 944 +7463 944 +7463 12234 +4000000 12234 + diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..a58943a48f97b8f2d3333cf34f4a28b685cf1127 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 2 (recommended) +The proportion of truncated or collapsed SFS types: 0.031746031746031744 + diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/receipt_51935243.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/receipt_51935243.json new file mode 100644 index 0000000000000000000000000000000000000000..3639d95f986bd60f3696a19430276c497d328d45 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/receipt_51935243.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "a546b4c699028ab4ad5afd419550d03d1c3f53b6744455f2335954bf1efd94c8", + "elapsed_s": 827, + "failure_sha256": null, + "host": "cn504-18", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935243", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "7c925015303cf7691bd24ada2d9c75eb42edcde5a69d7e3e4e0a406ae7e4a58c", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:09:44Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..9daf868299e5d22ecc3bafaaa7f7cf4346b1ada2 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g0/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g0/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_5K/receipts/export_51933159.json"], "job_id": "51935243", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X10_5K/fitcoal_g0.json", "request_sha256": "4e8b69745de4254080e2184018e00635b0fb4c0346af349971af73b20cadbf2e", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [0], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "7c925015303cf7691bd24ada2d9c75eb42edcde5a69d7e3e4e0a406ae7e4a58c", "stage": "v2", "usage_before": {"account_jobs": 163, "bench_cores": 475, "bench_gpus": 19, "bench_jobs": 92, "bench_pending": 40, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:33:27Z"} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/envlock_check_51935245.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/envlock_check_51935245.json new file mode 100644 index 0000000000000000000000000000000000000000..a92f157693b5100f21444fb0bc2c7bb66ebf3065 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/envlock_check_51935245.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn504-18", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935245", + "status": "PASS", + "utc": "20260916T115603Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..a0847a7b89441d4c788e18e5f84558308e3299da --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X10_5K", + "g": 1, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_5K/r00000001/n32" + ], + "rep": 1, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..98065173fb30399689e847cdaacb01673f672ddd --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +13388 6567 3873 2806 2082 1738 1533 1192 960 764 683 656 523 540 560 434 403 383 396 330 378 380 352 395 288 300 302 295 275 233 181 230 179 245 236 245 238 267 216 281 254 260 263 210 269 222 212 204 253 221 213 189 228 154 185 227 280 246 238 200 211 178 184 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..5fd745d98d039e234f91e04d4d11efc13f57b265 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g1/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g1/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 1 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..00b6a00fef35a806b417401d40197bcf531cba81 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 7,110 changeTypes: 0 +maxLogL = -1548.4061099796186 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 10,101 changeTypes: 1 +standardTime: 0.10322871624361671 generations: 2085.45 N: 5,755 changeTypes: 0 +maxLogL = -672.0158826062027 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 9,646 changeTypes: 1 +standardTime: 0.3034813646313643 generations: 5855.00 N: 112 changeTypes: 1 +standardTime: 1.1704564670159414 generations: 6049.24 N: 11,202 changeTypes: 0 +maxLogL = -383.9982890546788 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 7,020 changeTypes: 2 +standardTime: 0.006458188671422213 generations: 107.32 N: 9,932 changeTypes: 1 +standardTime: 0.2672355641751199 generations: 5287.65 N: 1,194 changeTypes: 1 +standardTime: 1.4297525552038235 generations: 8062.80 N: 12,964 changeTypes: 0 +maxLogL = -381.96562016319604 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 9,646 changeTypes: 1 +standardTime: 0.3034813646313643 generations: 5855.00 N: 112 changeTypes: 1 +standardTime: 1.1704564670159414 generations: 6049.24 N: 11,202 changeTypes: 0 +maxLogL = -383.9982890546788 + +computing time = 834.69 seconds diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..23b57d236fe92fbb2f82462dc18cbdf93a23204e --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fitcoal/output.txt @@ -0,0 +1,8 @@ +year popSize +2000 9646 +5855 9646 +5855 112 +6049 112 +6049 11202 +4000000 11202 + diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/receipt_51935245.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/receipt_51935245.json new file mode 100644 index 0000000000000000000000000000000000000000..d6c95237e0aaed6bc6b8b0f96a9a3dc17735c269 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/receipt_51935245.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "e39ca0ebfb474051b747ef62eda1e8d3ca3b01214af925c2f82193ed1dc74341", + "elapsed_s": 851, + "failure_sha256": null, + "host": "cn504-18", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935245", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "f1922fcb6f0eb1bc1c2397820a3ce35de46b1ad5aea933db9ff8a8e7419390ab", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:10:08Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..a9a14a7437370f6b1ce00ec507397ac33ed36432 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g1/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g1/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_5K/receipts/export_51933159.json"], "job_id": "51935245", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X10_5K/fitcoal_g1.json", "request_sha256": "8628e250a730995e97550c536e7c929473bff52694dd774e5828cfc845a6e2cd", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [1], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "f1922fcb6f0eb1bc1c2397820a3ce35de46b1ad5aea933db9ff8a8e7419390ab", "stage": "v2", "usage_before": {"account_jobs": 163, "bench_cores": 476, "bench_gpus": 19, "bench_jobs": 92, "bench_pending": 41, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:33:31Z"} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/envlock_check_51935251.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/envlock_check_51935251.json new file mode 100644 index 0000000000000000000000000000000000000000..99b6042cd6315c7ee945410d15d08c27c81f6a77 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/envlock_check_51935251.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn504-18", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935251", + "status": "PASS", + "utc": "20260916T115603Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..453c52025a2c80eee22f5a4efe249defa59bf50f --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X10_5K", + "g": 2, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_5K/r00000002/n32" + ], + "rep": 2, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..9400a6bfe2becdc73ad58f29b8c15ff81e091b3b --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +13909 6698 4187 2867 2341 1653 1289 1077 1089 840 722 695 657 580 534 452 455 456 368 466 453 381 367 349 366 374 349 327 271 329 276 300 303 316 281 303 309 312 326 284 310 279 295 307 243 254 263 185 248 234 244 222 185 240 267 193 197 212 246 215 208 200 146 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..3a4c7ec599016e7dbe3fdb8a54929ebe07b4f103 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g2/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g2/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 1 -randSeed 2 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..d9d1cdccf001a42b543af0b9f1605985ce26b5c7 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 7,520 changeTypes: 0 +maxLogL = -1325.6442062043943 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 10,668 changeTypes: 1 +standardTime: 0.07939516099521556 generations: 1693.93 N: 6,353 changeTypes: 0 +maxLogL = -618.4864173603 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 10,255 changeTypes: 1 +standardTime: 0.23653036445777612 generations: 4851.29 N: 111 changeTypes: 1 +standardTime: 0.7065830868865844 generations: 4956.03 N: 9,004 changeTypes: 0 +maxLogL = -337.7981095913799 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 8,546 changeTypes: 2 +standardTime: 0.03780374174716805 generations: 746.32 N: 11,485 changeTypes: 1 +standardTime: 0.2000904387144711 generations: 4473.97 N: 130 changeTypes: 1 +standardTime: 0.6417234883147683 generations: 4588.77 N: 8,710 changeTypes: 0 +maxLogL = -328.64616270551403 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 10,255 changeTypes: 1 +standardTime: 0.23653036445777612 generations: 4851.29 N: 111 changeTypes: 1 +standardTime: 0.7065830868865844 generations: 4956.03 N: 9,004 changeTypes: 0 +maxLogL = -337.7981095913799 + +computing time = 831.72 seconds diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..40dc8e383991dd58bf82d4b575ac105ebcd4bde8 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fitcoal/output.txt @@ -0,0 +1,8 @@ +year popSize +2000 10255 +4851 10255 +4851 111 +4956 111 +4956 9004 +4000000 9004 + diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..5dc872fd79c57a0630616d4dc65b24263eb0d126 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 1 (recommended) +The proportion of truncated or collapsed SFS types: 0.015873015873015872 + diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/receipt_51935251.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/receipt_51935251.json new file mode 100644 index 0000000000000000000000000000000000000000..3d4a37174b204450117e7a1152860ca08963221e --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/receipt_51935251.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "73f53463796ff6ab3bb98330a4bb3fb152405d0f8944cafc01a434cba9858c38", + "elapsed_s": 848, + "failure_sha256": null, + "host": "cn504-18", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935251", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "c3539d74910764d35d93f4d09cbb5725a2f6e20a95b4902beec191f113c993ae", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:10:05Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..96b6ff7b58418105b89e61608af9018ae52a3d5a --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g2/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g2/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_5K/receipts/export_51933159.json"], "job_id": "51935251", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X10_5K/fitcoal_g2.json", "request_sha256": "809618a33746740ece9fbf10ef04c51b42910257a7cec620789ea46d05dcf749", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [2], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "c3539d74910764d35d93f4d09cbb5725a2f6e20a95b4902beec191f113c993ae", "stage": "v2", "usage_before": {"account_jobs": 164, "bench_cores": 478, "bench_gpus": 19, "bench_jobs": 93, "bench_pending": 42, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:33:35Z"} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/envlock_check_51935255.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/envlock_check_51935255.json new file mode 100644 index 0000000000000000000000000000000000000000..b8cfbc8b552b894b348cf0590e230ca93000c26e --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/envlock_check_51935255.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn504-17", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935255", + "status": "PASS", + "utc": "20260916T115557Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..20aa0a6a56f025f985f1bc7caff9f1eb1cf2e077 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X10_5K", + "g": 3, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_5K/r00000003/n32" + ], + "rep": 3, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..75a9564dca734f512fbe138155a97add97165d11 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +13543 6188 3915 2807 2157 1756 1467 1126 969 884 722 713 614 527 446 449 441 363 366 370 393 378 354 335 320 242 281 294 243 249 222 263 219 229 238 247 296 212 231 222 216 306 288 234 238 224 256 218 198 217 230 195 189 210 211 244 262 204 197 253 237 193 177 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..df34fa2d0b31c31e91656728addc62c94034e85e --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g3/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g3/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 3 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..5756ed2baff96483111427bbacbde7c9e731f81a --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 7,119 changeTypes: 0 +maxLogL = -1454.9418122061861 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 10,050 changeTypes: 1 +standardTime: 0.1004909656054562 generations: 2019.94 N: 5,818 changeTypes: 0 +maxLogL = -633.3767774788392 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 9,541 changeTypes: 1 +standardTime: 0.3185176242900821 generations: 6077.65 N: 134 changeTypes: 1 +standardTime: 1.3404830783350108 generations: 6351.67 N: 13,034 changeTypes: 0 +maxLogL = -334.5133318122381 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 11,988 changeTypes: 2 +standardTime: 0.004971413676468478 generations: 105.28 N: 9,399 changeTypes: 1 +standardTime: 0.32698292462197354 generations: 6158.58 N: 207 changeTypes: 1 +standardTime: 1.4414644121106095 generations: 6620.76 N: 14,145 changeTypes: 0 +maxLogL = -333.55463931615293 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 9,541 changeTypes: 1 +standardTime: 0.3185176242900821 generations: 6077.65 N: 134 changeTypes: 1 +standardTime: 1.3404830783350108 generations: 6351.67 N: 13,034 changeTypes: 0 +maxLogL = -334.5133318122381 + +computing time = 760.88 seconds diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..89bad70f6bad9bf4eed05457f713a0a929cb3b79 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fitcoal/output.txt @@ -0,0 +1,8 @@ +year popSize +2000 9541 +6078 9541 +6078 134 +6352 134 +6352 13034 +4000000 13034 + diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/receipt_51935255.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/receipt_51935255.json new file mode 100644 index 0000000000000000000000000000000000000000..152c0b8286a4c1b7d7177b0bc88e12bea9c1e93a --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/receipt_51935255.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "4577812d9d45dbeed3f44ed255f080d86868a13e76cc29bdfb1b012e571ac57f", + "elapsed_s": 776, + "failure_sha256": null, + "host": "cn504-17", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935255", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "4242b4e14f6dd7ad6f5baf4499d0c0811a18226b26a10af01d75160acc0520bd", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:08:53Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..c0a9cecc2b684e208edddfe309b795c11a5284b5 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g3/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g3/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_5K/receipts/export_51933159.json"], "job_id": "51935255", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X10_5K/fitcoal_g3.json", "request_sha256": "a8d026af282829ece3dc8b99c8343596f662587224650954bdb9ac1dc6ddd07a", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [3], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "4242b4e14f6dd7ad6f5baf4499d0c0811a18226b26a10af01d75160acc0520bd", "stage": "v2", "usage_before": {"account_jobs": 165, "bench_cores": 480, "bench_gpus": 19, "bench_jobs": 94, "bench_pending": 43, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:33:39Z"} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/envlock_check_51935259.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/envlock_check_51935259.json new file mode 100644 index 0000000000000000000000000000000000000000..e8d4d7585b61792ad88e09886a12f2bab1f4c0a4 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/envlock_check_51935259.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn504-17", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935259", + "status": "PASS", + "utc": "20260916T115557Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..e25f17d5b00645ccb0afcbb82937d981adc14d35 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X10_5K", + "g": 4, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_5K/r00000004/n32" + ], + "rep": 4, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..7f0de76348ce6abcf236b42d774151e212a79dd6 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +14048 6500 4342 2857 2175 1727 1409 1256 1018 785 818 600 572 554 490 466 387 390 362 388 375 358 317 284 335 357 251 255 301 325 266 232 228 292 246 224 243 300 262 229 265 226 267 227 224 223 229 303 219 246 199 190 201 210 208 230 253 215 213 222 288 159 243 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..02f7447b10c6fca589d78b89ae271324d48dbfbc --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g4/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g4/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 3 -randSeed 4 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..11b012d924e3ede1e378f9fdd7209feccb344599 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 7,321 changeTypes: 0 +maxLogL = -1620.3804070397946 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 10,572 changeTypes: 1 +standardTime: 0.10518377028870418 generations: 2224.10 N: 5,804 changeTypes: 0 +maxLogL = -597.1974366421374 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 10,126 changeTypes: 1 +standardTime: 0.287318532740602 generations: 5818.91 N: 120 changeTypes: 1 +standardTime: 1.1348617279422832 generations: 6023.06 N: 11,263 changeTypes: 0 +maxLogL = -321.0727842847432 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 9,802 changeTypes: 1 +standardTime: 0.1304653633273656 generations: 2557.73 N: 117,979 changeTypes: 2 +standardTime: 0.2566734019460651 generations: 4768.03 N: 2,146 changeTypes: 1 +standardTime: 1.9304793622395235 generations: 11950.35 N: 18,741 changeTypes: 0 +maxLogL = -318.05572988118 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 10,126 changeTypes: 1 +standardTime: 0.287318532740602 generations: 5818.91 N: 120 changeTypes: 1 +standardTime: 1.1348617279422832 generations: 6023.06 N: 11,263 changeTypes: 0 +maxLogL = -321.0727842847432 + +computing time = 772.32 seconds diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..3cd6c0a96b3e7460850cd1bcdea065d7b893943d --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fitcoal/output.txt @@ -0,0 +1,8 @@ +year popSize +2000 10126 +5819 10126 +5819 120 +6023 120 +6023 11263 +4000000 11263 + diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..47de88aebecef4006ba97a94faaf20de764f8f92 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 3 (recommended) +The proportion of truncated or collapsed SFS types: 0.047619047619047616 + diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/receipt_51935259.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/receipt_51935259.json new file mode 100644 index 0000000000000000000000000000000000000000..36e1271006f94cf7942e90602ddfb6efb2365f1b --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/receipt_51935259.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "92a8ac3e47d4d057e1596567ad1a055c0a38b1a84b3e64724bd3c54c966f4064", + "elapsed_s": 788, + "failure_sha256": null, + "host": "cn504-17", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935259", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "aed11e7844c65479280ce3408343d5ccecfeb9befc009a8856b2fcb593493a3e", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:09:05Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..d5c6315a9de9b2840434e787201f33d8424841cc --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g4/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g4/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_5K/receipts/export_51933159.json"], "job_id": "51935259", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X10_5K/fitcoal_g4.json", "request_sha256": "573b5e608ffbf80027e5a601fa8bde5a1f22c1f187ffb5ee1b5599d778d4819f", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [4], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "aed11e7844c65479280ce3408343d5ccecfeb9befc009a8856b2fcb593493a3e", "stage": "v2", "usage_before": {"account_jobs": 166, "bench_cores": 482, "bench_gpus": 19, "bench_jobs": 95, "bench_pending": 44, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:33:43Z"} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/envlock_check_51935261.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/envlock_check_51935261.json new file mode 100644 index 0000000000000000000000000000000000000000..6b0c790356394d3f10e935e2fa4e0b55cd5b0b3d --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/envlock_check_51935261.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn504-17", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935261", + "status": "PASS", + "utc": "20260916T115558Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..2827658944d7ebb94d45dadf3b4472459c447c1b --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X10_5K", + "g": 5, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_5K/r00000005/n32" + ], + "rep": 5, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..2509c09c815c3b8d766620295f87bdeae3932075 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +14029 6521 4122 2658 2134 1656 1355 1190 986 923 702 621 646 539 545 542 451 419 430 359 359 310 316 319 311 325 301 356 320 289 318 264 304 274 280 270 256 260 201 212 220 221 216 237 251 258 229 275 266 245 253 193 210 266 248 266 252 234 235 217 292 228 222 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..def6e82b9e6fbaf928c54177eaff5b21d86c18fe --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g5/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g5/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 3 -randSeed 5 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..e90967ba7293122c4c1c6b0fbcce4c61ed518c4b --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 7,331 changeTypes: 0 +maxLogL = -1468.0296921215545 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 10,789 changeTypes: 1 +standardTime: 0.07927339713070859 generations: 1710.53 N: 6,038 changeTypes: 0 +maxLogL = -593.477603611401 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 10,067 changeTypes: 1 +standardTime: 0.23637184444776016 generations: 4759.15 N: 2,030 changeTypes: 1 +standardTime: 1.9989995771465352 generations: 11915.37 N: 21,326 changeTypes: 0 +maxLogL = -309.2933546622187 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 10,248 changeTypes: 1 +standardTime: 0.13292464568789877 generations: 2724.29 N: 6,591 changeTypes: 1 +standardTime: 0.4401343176437076 generations: 6773.82 N: 240 changeTypes: 1 +standardTime: 1.9504570429165005 generations: 7497.40 N: 23,954 changeTypes: 0 +maxLogL = -306.1837576689825 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 10,067 changeTypes: 1 +standardTime: 0.23637184444776016 generations: 4759.15 N: 2,030 changeTypes: 1 +standardTime: 1.9989995771465352 generations: 11915.37 N: 21,326 changeTypes: 0 +maxLogL = -309.2933546622187 + +computing time = 800.65 seconds diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..43629d82f23309a921e48016f967b1270a9b1d3c --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fitcoal/output.txt @@ -0,0 +1,8 @@ +year popSize +2000 10067 +4759 10067 +4759 2030 +11915 2030 +11915 21326 +4000000 21326 + diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..47de88aebecef4006ba97a94faaf20de764f8f92 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 3 (recommended) +The proportion of truncated or collapsed SFS types: 0.047619047619047616 + diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/receipt_51935261.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/receipt_51935261.json new file mode 100644 index 0000000000000000000000000000000000000000..727947c20a5fb959ec57a146014d699935818e49 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/receipt_51935261.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "0db434919f23e4113f76ded4f1104278ba5162621c181fecef9537893e3f5f9b", + "elapsed_s": 816, + "failure_sha256": null, + "host": "cn504-17", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935261", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "cafb19edc6b28f9b326d4c1156ccd9239809fe7fc8334f7b029b247532e04cdd", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:09:33Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..de10a20cbd78ac005665ea51b878b054dffebfdd --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g5/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g5/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_5K/receipts/export_51933159.json"], "job_id": "51935261", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X10_5K/fitcoal_g5.json", "request_sha256": "ed1644dc9c10f5bcc564aa111d6a48fe2f45cd3f3b971df63dd901eed7148e25", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [5], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "cafb19edc6b28f9b326d4c1156ccd9239809fe7fc8334f7b029b247532e04cdd", "stage": "v2", "usage_before": {"account_jobs": 167, "bench_cores": 484, "bench_gpus": 19, "bench_jobs": 96, "bench_pending": 45, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:33:47Z"} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/envlock_check_51935264.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/envlock_check_51935264.json new file mode 100644 index 0000000000000000000000000000000000000000..5442eb573134815f46e0606ed07144bb6263edc6 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/envlock_check_51935264.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn511-12", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935264", + "status": "PASS", + "utc": "20260916T120020Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..1b9a5d63e3b4a4f9010c8a8a0cda3a3938ca0843 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X10_5K", + "g": 6, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_5K/r00000006/n32" + ], + "rep": 6, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..081e1ca86d06c682fe415fd6ddf82d5b4b44ed33 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +14326 6643 3984 2947 2109 1610 1370 1093 948 800 644 654 617 552 466 435 486 419 377 400 363 433 369 310 350 335 332 323 327 336 298 301 260 281 309 294 275 292 264 181 238 330 267 255 243 244 251 215 188 235 219 197 190 199 215 221 205 205 154 201 249 194 191 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..dc3ac5e853cec3dd547cfdda21b2d7e8375a4e2a --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g6/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g6/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 3 -randSeed 6 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..4d4b8a4e8bd7ddb9b77e50e52fd78f538a5ce360 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 7,348 changeTypes: 0 +maxLogL = -1555.818806138876 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 11,145 changeTypes: 1 +standardTime: 0.0782670040302058 generations: 1744.55 N: 5,942 changeTypes: 0 +maxLogL = -520.5706169833619 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 10,612 changeTypes: 1 +standardTime: 0.20702306221971148 generations: 4393.82 N: 106 changeTypes: 1 +standardTime: 0.6046061981471482 generations: 4478.21 N: 7,901 changeTypes: 0 +maxLogL = -309.0789485207664 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 9,851 changeTypes: 2 +standardTime: 0.16853228912903565 generations: 4071.55 N: 15,034 changeTypes: 2 +standardTime: 0.1929444372402376 generations: 4105.69 N: 150 changeTypes: 1 +standardTime: 0.55910737406604 generations: 4215.79 N: 7,735 changeTypes: 0 +maxLogL = -305.266623969943 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 10,612 changeTypes: 1 +standardTime: 0.20702306221971148 generations: 4393.82 N: 106 changeTypes: 1 +standardTime: 0.6046061981471482 generations: 4478.21 N: 7,901 changeTypes: 0 +maxLogL = -309.0789485207664 + +computing time = 739.64 seconds diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..c19f8cc00fb2ccb91dab7b68d0e18ea658f7168f --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fitcoal/output.txt @@ -0,0 +1,8 @@ +year popSize +2000 10612 +4394 10612 +4394 106 +4478 106 +4478 7901 +4000000 7901 + diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..47de88aebecef4006ba97a94faaf20de764f8f92 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 3 (recommended) +The proportion of truncated or collapsed SFS types: 0.047619047619047616 + diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/receipt_51935264.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/receipt_51935264.json new file mode 100644 index 0000000000000000000000000000000000000000..584f02de3b79ee449d8a8f7bcdbdafe5709e112a --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/receipt_51935264.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "ae7c1e58ac4788981dacb4868a927312875d49909c8c1afb7b32721a22cb435b", + "elapsed_s": 882, + "failure_sha256": null, + "host": "cn511-12", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935264", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "9a29ecce11c3246ff4b595f13a981b6f18d03db4f78a2ede8fd9b226e000d865", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:12:56Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..ea5b84d8ec198557ae54082f9446124ab208899c --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g6/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g6/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_5K/receipts/export_51933159.json"], "job_id": "51935264", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X10_5K/fitcoal_g6.json", "request_sha256": "691b364eea216e0c47b526f689d8bdab2438153c3a497b232f7ec9775887814a", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [6], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "9a29ecce11c3246ff4b595f13a981b6f18d03db4f78a2ede8fd9b226e000d865", "stage": "v2", "usage_before": {"account_jobs": 167, "bench_cores": 478, "bench_gpus": 19, "bench_jobs": 96, "bench_pending": 46, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:33:51Z"} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/envlock_check_51935270.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/envlock_check_51935270.json new file mode 100644 index 0000000000000000000000000000000000000000..b28480f2552806354b5f3fdb7becc9b9492c1e98 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/envlock_check_51935270.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn504-14", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51935270", + "status": "PASS", + "utc": "20260916T120705Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fit_spec.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..5af1209c04081734d43788d801279a69d7488cb2 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_BOT_X10_5K", + "g": 7, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_5K/r00000007/n32" + ], + "rep": 7, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..7cefb7c9b717f8249885322cef462ee4381a6986 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +13681 6607 4003 2705 2147 1640 1301 1150 993 874 775 632 609 529 525 440 450 384 361 379 379 369 371 355 361 354 367 320 305 306 276 316 314 264 284 314 321 298 325 271 287 245 273 278 185 234 249 210 216 231 224 213 248 228 189 240 219 213 212 214 242 231 198 \ No newline at end of file diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..74ead70b2d1456f8e88aa94ba5e446a3164db80d --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g7/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g7/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 7 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..48232c96131c45003b6ab42bdc6b55f98d96eee6 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 7,322 changeTypes: 0 +maxLogL = -1353.3742412120625 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 10,582 changeTypes: 1 +standardTime: 0.07449787760754853 generations: 1576.62 N: 6,178 changeTypes: 0 +maxLogL = -623.2780697838253 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 10,042 changeTypes: 1 +standardTime: 0.23856579033935177 generations: 4791.56 N: 109 changeTypes: 1 +standardTime: 0.7617598842659516 generations: 4905.23 N: 9,117 changeTypes: 0 +maxLogL = -312.6423828853726 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 7,717 changeTypes: 2 +standardTime: 0.010656597853228283 generations: 190.79 N: 10,465 changeTypes: 1 +standardTime: 0.2217282375348756 generations: 4608.48 N: 173 changeTypes: 1 +standardTime: 0.7325125649002443 generations: 4785.39 N: 8,959 changeTypes: 0 +maxLogL = -309.1068825459729 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 10,042 changeTypes: 1 +standardTime: 0.23856579033935177 generations: 4791.56 N: 109 changeTypes: 1 +standardTime: 0.7617598842659516 generations: 4905.23 N: 9,117 changeTypes: 0 +maxLogL = -312.6423828853726 + +computing time = 752.57 seconds diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fitcoal/output.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..74c0cb5cd51a21a7c482d2d1edba4475e3632195 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fitcoal/output.txt @@ -0,0 +1,8 @@ +year popSize +2000 10042 +4792 10042 +4792 109 +4905 109 +4905 9117 +4000000 9117 + diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/receipt_51935270.json b/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/receipt_51935270.json new file mode 100644 index 0000000000000000000000000000000000000000..438b88203515e218203b440fa93d6c6d6fc18aa3 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/receipt_51935270.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "65f6c84641c9b3537c1eba905ca30b43394e2389cd15dd83ce1e883faa45b2f7", + "elapsed_s": 1299, + "failure_sha256": null, + "host": "cn504-14", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51935270", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "a9dfc43c276a96ee84906fcb01b1ea14703d3ec61338b14fa6131ad870bbc2b0", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:19:53Z" +} diff --git a/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/submissions.jsonl b/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..908d05e3e1a6ac4d521e1136a6b3f188c3863dc6 --- /dev/null +++ b/estimates/fitcoal/a1/BOT_X10_5K/K1/g7/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_BOT_X10_5K/K1/g7/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_BOT_X10_5K/receipts/export_51933159.json"], "job_id": "51935270", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_BOT_X10_5K/fitcoal_g7.json", "request_sha256": "d6e305c63b2520a0f7fa271c36155c1f1779f8ed2fd4dee9d68d9faef2f26406", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [7], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "a9dfc43c276a96ee84906fcb01b1ea14703d3ec61338b14fa6131ad870bbc2b0", "stage": "v2", "usage_before": {"account_jobs": 168, "bench_cores": 480, "bench_gpus": 19, "bench_jobs": 97, "bench_pending": 47, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:33:55Z"} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/envlock_check_51945170.json b/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/envlock_check_51945170.json new file mode 100644 index 0000000000000000000000000000000000000000..d047661d0568cc8695cb535f1848ed97c85d1a4a --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/envlock_check_51945170.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-12", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51945170", + "status": "PASS", + "utc": "20260916T124540Z" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fit_spec.json b/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..2fd92f9893015763dd0c9e5aef099785e11a0cec --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_CONST_2K", + "g": 0, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_2K/r00000000/n32" + ], + "rep": 0, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..9be1a8457923b0f0621eead0762614df67dc3309 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +2827 1518 929 721 573 484 431 372 336 305 279 280 248 180 219 168 157 145 171 155 126 156 129 100 126 128 126 137 103 104 103 70 91 80 95 109 80 104 68 51 62 89 58 69 67 48 46 56 62 39 66 36 52 45 55 55 47 33 54 27 69 55 41 \ No newline at end of file diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..2285f5ab67928c3d51a06317240dd9375896fd89 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g0/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g0/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 3 -randSeed 0 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..b00c860ab8338dd100e527437fe17eaa0f90b6b5 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fitcoal/decoder.out @@ -0,0 +1,16 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 1,944 changeTypes: 0 +maxLogL = -271.8379019405905 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 1,615 changeTypes: 2 +standardTime: 0.015481604902103256 generations: 55.02 N: 1,961 changeTypes: 0 +maxLogL = -270.42305677526036 + +******** Best: ******** +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 1,944 changeTypes: 0 +maxLogL = -271.8379019405905 + +computing time = 14.80 seconds diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fitcoal/output.txt b/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..ba8c9c2d166217e3c40875ef11bb98edc94cf063 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 1944 +4000000 1944 + diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..47de88aebecef4006ba97a94faaf20de764f8f92 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 3 (recommended) +The proportion of truncated or collapsed SFS types: 0.047619047619047616 + diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/receipt_51945170.json b/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/receipt_51945170.json new file mode 100644 index 0000000000000000000000000000000000000000..b781407b4f1bd0b9f2893e1d705cf862f3b12ad6 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/receipt_51945170.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "1ac302865956bc7474f85d836f6024c144dcade266e7b218cb65b320d1c08701", + "elapsed_s": 27, + "failure_sha256": null, + "host": "cn604-12", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51945170", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "f1e39c20fc7b465454c2266fc3a1228740acec2579c6fbd4dc6a341cf05dd658", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:46:04Z" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/submissions.jsonl b/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..5a63b7de75f585d8f9eaef650de35f2e4f43b738 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g0/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g0/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_2K/receipts/export_51933476.json"], "job_id": "51945170", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_CONST_2K/fitcoal_g0.json", "request_sha256": "687122167121c40fad6bcda666e65bfc226319f3293195b773387f06b9e06ab9", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [0], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "f1e39c20fc7b465454c2266fc3a1228740acec2579c6fbd4dc6a341cf05dd658", "stage": "v2", "usage_before": {"account_jobs": 160, "bench_cores": 615, "bench_gpus": 11, "bench_jobs": 108, "bench_pending": 7, "never_startable_pending": 0, "throttle_held_not_counted": 5}, "utc": "2026-09-16T12:45:20Z"} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/envlock_check_51945180.json b/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/envlock_check_51945180.json new file mode 100644 index 0000000000000000000000000000000000000000..8c69377779fa87e25cc716d2d71bad4d1bb98844 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/envlock_check_51945180.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-09", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51945180", + "status": "PASS", + "utc": "20260916T124711Z" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fit_spec.json b/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..72b94cf2637391be431f59069a21469aae4d1c59 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_CONST_2K", + "g": 1, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_2K/r00000001/n32" + ], + "rep": 1, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..69aa39aa040f789d44e9568818949b5c52e3a08d --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +2901 1530 1000 871 568 470 475 360 294 296 259 272 233 226 206 185 163 148 138 149 117 143 116 122 136 92 96 107 75 106 110 88 73 67 64 89 79 55 83 75 82 80 82 72 68 51 53 63 74 55 69 45 38 74 54 58 66 44 50 66 49 29 69 \ No newline at end of file diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..ebf37dc2cddebb16bc3a0482bcf0e4d1f576544f --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g1/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g1/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 1 -randSeed 1 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..5b1230074f61611b9eb0c3108c56d647a271f0d3 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fitcoal/decoder.out @@ -0,0 +1,16 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 1,975 changeTypes: 0 +maxLogL = -277.38968177928876 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 2,008 changeTypes: 1 +standardTime: 0.3955898698592994 generations: 1588.77 N: 1,931 changeTypes: 0 +maxLogL = -276.1872583415659 + +******** Best: ******** +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 1,975 changeTypes: 0 +maxLogL = -277.38968177928876 + +computing time = 41.23 seconds diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fitcoal/output.txt b/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..a4d74f17de27a879f96118fdc8cc9b4ac3b1932a --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 1975 +4000000 1975 + diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..5dc872fd79c57a0630616d4dc65b24263eb0d126 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 1 (recommended) +The proportion of truncated or collapsed SFS types: 0.015873015873015872 + diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/receipt_51945180.json b/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/receipt_51945180.json new file mode 100644 index 0000000000000000000000000000000000000000..d9c0417f92be080df58fe4043aa811df27df5ef5 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/receipt_51945180.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "c7f11945d80ef89ad80b23e40d41d83a30cd2253008b70a3749df40747f779a2", + "elapsed_s": 138, + "failure_sha256": null, + "host": "cn604-09", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51945180", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "39b173ffabce890d66acd5d88c2d48d2e3433b4d48dac700d514cc4dc353b69c", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:48:00Z" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/submissions.jsonl b/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..2fff71641f19e2285b707f03c44e3ad73a9e090d --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g1/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g1/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_2K/receipts/export_51933476.json"], "job_id": "51945180", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_CONST_2K/fitcoal_g1.json", "request_sha256": "70ae4bbe6fa45a58966064605c625dceb0cf3250d1257e60d0dca2092b6b32cc", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [1], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "39b173ffabce890d66acd5d88c2d48d2e3433b4d48dac700d514cc4dc353b69c", "stage": "v2", "usage_before": {"account_jobs": 159, "bench_cores": 609, "bench_gpus": 9, "bench_jobs": 107, "bench_pending": 7, "never_startable_pending": 0, "throttle_held_not_counted": 5}, "utc": "2026-09-16T12:45:26Z"} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/envlock_check_51945187.json b/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/envlock_check_51945187.json new file mode 100644 index 0000000000000000000000000000000000000000..5c8f097c5db847cfd844fa11ade960876f843058 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/envlock_check_51945187.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-11", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51945187", + "status": "PASS", + "utc": "20260916T124550Z" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fit_spec.json b/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..76fb0856432afaf451521788d5ae747d393aae88 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_CONST_2K", + "g": 2, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_2K/r00000002/n32" + ], + "rep": 2, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..825b27bb09252e83d5227a6e7a684b782c1a29aa --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +2934 1641 998 700 632 537 412 423 347 295 301 280 239 213 201 197 207 170 147 155 162 123 149 129 84 145 98 111 111 89 83 120 71 95 86 113 78 90 60 76 78 77 73 84 104 69 59 51 62 43 71 52 55 56 61 50 60 75 52 59 47 44 51 \ No newline at end of file diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..b852224bce907684cb4db4b612de4ff7e02067fb --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g2/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g2/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 2 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..7c5eb481d636ae972678a112e195597d36d522b9 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fitcoal/decoder.out @@ -0,0 +1,16 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 2,049 changeTypes: 0 +maxLogL = -279.89758884636245 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 1,581 changeTypes: 2 +standardTime: 0.015811188688438636 generations: 57.09 N: 2,074 changeTypes: 0 +maxLogL = -276.878577538056 + +******** Best: ******** +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 2,049 changeTypes: 0 +maxLogL = -279.89758884636245 + +computing time = 14.88 seconds diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fitcoal/output.txt b/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..c0de361cfed4b05149d1e83404a8b40622fd8d70 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 2049 +4000000 2049 + diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/receipt_51945187.json b/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/receipt_51945187.json new file mode 100644 index 0000000000000000000000000000000000000000..9fd9cd934fb1be5767c7c0ac5e0aacd84e588beb --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/receipt_51945187.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "87e5b15b3036c23a856acdc08c6acb5aa45f5369b4c3e05954032b7fd38bbb8f", + "elapsed_s": 28, + "failure_sha256": null, + "host": "cn604-11", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51945187", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "3885066492ccafd51a99f6481201b7c444147b89526be26b852998d9c003f99c", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:46:16Z" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/submissions.jsonl b/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..76dc67b1079ba512296c014777305f2a2f5bdfd5 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g2/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g2/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_2K/receipts/export_51933476.json"], "job_id": "51945187", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_CONST_2K/fitcoal_g2.json", "request_sha256": "701fbb32e6f848c505f3e65e0a0ca5670f5ab9374954d5e9f9ab2c8c9a186ecc", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [2], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "3885066492ccafd51a99f6481201b7c444147b89526be26b852998d9c003f99c", "stage": "v2", "usage_before": {"account_jobs": 158, "bench_cores": 605, "bench_gpus": 8, "bench_jobs": 106, "bench_pending": 7, "never_startable_pending": 0, "throttle_held_not_counted": 5}, "utc": "2026-09-16T12:45:32Z"} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/envlock_check_51945278.json b/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/envlock_check_51945278.json new file mode 100644 index 0000000000000000000000000000000000000000..d549a22d41fa4c25b1f291e557933dab9b8a6e57 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/envlock_check_51945278.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-13", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51945278", + "status": "PASS", + "utc": "20260916T124627Z" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fit_spec.json b/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..1dbff811076ab44f3bb3c9591c4705ed81c8b723 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_CONST_2K", + "g": 3, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_2K/r00000003/n32" + ], + "rep": 3, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..98d44f54c84da2139239206e9b2544f6e7a442cd --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +3142 1500 1055 724 625 516 418 388 297 232 298 270 242 216 170 199 183 152 175 172 147 149 138 116 126 81 93 89 74 85 79 82 73 73 85 85 82 77 61 64 80 64 77 64 94 65 52 53 50 50 62 65 73 58 65 61 44 66 71 37 66 43 46 \ No newline at end of file diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..9ed9cd61fef4f550574836038e00681e07ba38ad --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g3/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g3/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 3 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..b22909ae8c6863a5c2af111daf3296387c44d599 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fitcoal/decoder.out @@ -0,0 +1,16 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 2,008 changeTypes: 0 +maxLogL = -283.44775960413494 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 2,134 changeTypes: 2 +standardTime: 0.260885619859661 generations: 1063.86 N: 1,949 changeTypes: 0 +maxLogL = -278.6520725585291 + +******** Best: ******** +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 2,008 changeTypes: 0 +maxLogL = -283.44775960413494 + +computing time = 26.97 seconds diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fitcoal/output.txt b/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..cc48128a8f209b6f441864af6e5554da75f42fcb --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 2008 +4000000 2008 + diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/receipt_51945278.json b/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/receipt_51945278.json new file mode 100644 index 0000000000000000000000000000000000000000..e1f5084676545526d4c3792c3167e9a8c5cd5e7e --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/receipt_51945278.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "bd247226eeaecbad1f994f33525dc32de5745c3d6fc98aea583494317542f98f", + "elapsed_s": 44, + "failure_sha256": null, + "host": "cn604-13", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51945278", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "ec63fe37339464b799879bc2aa7fd9026688b6ed5a17214eccbd79bc43bafb36", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:47:06Z" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/submissions.jsonl b/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..e3a571b30be718cabc28501f143ca69cbcea2677 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g3/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g3/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_2K/receipts/export_51933476.json"], "job_id": "51945278", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_CONST_2K/fitcoal_g3.json", "request_sha256": "27df8043d4f97c555e01c425ba9313f9e846064293f671503ad83dce2535b5ac", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [3], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "ec63fe37339464b799879bc2aa7fd9026688b6ed5a17214eccbd79bc43bafb36", "stage": "v2", "usage_before": {"account_jobs": 149, "bench_cores": 575, "bench_gpus": 2, "bench_jobs": 97, "bench_pending": 6, "never_startable_pending": 0, "throttle_held_not_counted": 5}, "utc": "2026-09-16T12:46:05Z"} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/envlock_check_51945283.json b/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/envlock_check_51945283.json new file mode 100644 index 0000000000000000000000000000000000000000..7422f2fd0faaa2fe63cd10cfb4e75d00c40c3e5b --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/envlock_check_51945283.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-12", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51945283", + "status": "PASS", + "utc": "20260916T124639Z" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fit_spec.json b/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..f7f0ceaa3981102e8f5046c4329477586df52ef8 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_CONST_2K", + "g": 4, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_2K/r00000004/n32" + ], + "rep": 4, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..341c8fea9da0c71bb3c26d9dad51441e72e8b4b0 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +3215 1602 955 766 572 454 419 295 294 247 246 213 224 214 216 187 202 193 148 163 108 121 173 129 78 113 67 79 107 113 104 85 83 84 71 68 58 73 48 95 56 57 69 90 72 75 96 49 73 53 40 52 45 52 57 39 58 37 51 41 29 49 47 \ No newline at end of file diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..06ce0977450c2f2b6da7c3931414cea6dade4aab --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g4/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g4/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 4 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..af00f95e49f054824c17c33cf434cb6c406f555d --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fitcoal/decoder.out @@ -0,0 +1,16 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 1,970 changeTypes: 0 +maxLogL = -332.5655275801059 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 2,326 changeTypes: 1 +standardTime: 0.05355924431370524 generations: 249.19 N: 1,873 changeTypes: 0 +maxLogL = -309.22259591715056 + +******** Best: ******** +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 1,970 changeTypes: 0 +maxLogL = -332.5655275801059 + +computing time = 19.42 seconds diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fitcoal/output.txt b/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..bbbbfc150d0bcfdb3ebdddc09b1216d07a928cb6 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 1970 +4000000 1970 + diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/receipt_51945283.json b/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/receipt_51945283.json new file mode 100644 index 0000000000000000000000000000000000000000..2c8ae39e48878696b30c36ffabd9170c8e5b3f6b --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/receipt_51945283.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "ecb6fbbccc620e62a6d6c5509103a1201e825c7f64ed117682396476603773b8", + "elapsed_s": 42, + "failure_sha256": null, + "host": "cn604-12", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51945283", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "df73d12a5e1a118a357b356aeb846a194de728488d9bcd56f3e8305c9f095422", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:47:09Z" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/submissions.jsonl b/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..133cd8cf1b0622ae58e297ff4d96a37cd22e8474 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g4/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g4/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_2K/receipts/export_51933476.json"], "job_id": "51945283", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_CONST_2K/fitcoal_g4.json", "request_sha256": "ab1de746292ad80f7a411a492c26eee07a1d4644548bb12531dc48909c3c3171", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [4], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "df73d12a5e1a118a357b356aeb846a194de728488d9bcd56f3e8305c9f095422", "stage": "v2", "usage_before": {"account_jobs": 147, "bench_cores": 571, "bench_gpus": 2, "bench_jobs": 95, "bench_pending": 6, "never_startable_pending": 0, "throttle_held_not_counted": 5}, "utc": "2026-09-16T12:46:11Z"} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/envlock_check_51945287.json b/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/envlock_check_51945287.json new file mode 100644 index 0000000000000000000000000000000000000000..987a4fb750c3330c2784100e12fc9efef078819a --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/envlock_check_51945287.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-12", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51945287", + "status": "PASS", + "utc": "20260916T124644Z" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fit_spec.json b/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..ab263a2cb4bfacd2a0390b2c8eb1d1c59b07d32c --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_CONST_2K", + "g": 5, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_2K/r00000005/n32" + ], + "rep": 5, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..6b59789a7e334e38b95eb0c2da4951fb13f76a6f --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +3150 1578 985 748 521 478 401 375 322 306 263 285 201 222 180 191 163 159 138 137 153 173 142 127 119 154 141 91 97 120 110 92 104 100 78 63 104 90 97 85 75 101 65 60 69 60 65 45 54 60 53 61 40 41 41 40 31 54 32 42 57 61 55 \ No newline at end of file diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..88e9c3e8d62fee576fdb0ee47722cdcac75fc3ff --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g5/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g5/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 4 -randSeed 5 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..0cd2da51cff64ad9f29359e1e551ad61a74b68fe --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fitcoal/decoder.out @@ -0,0 +1,16 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 2,014 changeTypes: 0 +maxLogL = -276.7388832485594 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 2,266 changeTypes: 1 +standardTime: 0.026915843306047234 generations: 121.98 N: 1,975 changeTypes: 0 +maxLogL = -271.75641311627896 + +******** Best: ******** +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 2,014 changeTypes: 0 +maxLogL = -276.7388832485594 + +computing time = 17.01 seconds diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fitcoal/output.txt b/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..561f1585bc0aa2da2a31f414a20652b385e26249 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 2014 +4000000 2014 + diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..f17274d89d9d62d06ab72eba6a878b5eb095d46b --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 4 (recommended) +The proportion of truncated or collapsed SFS types: 0.06349206349206349 + diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/receipt_51945287.json b/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/receipt_51945287.json new file mode 100644 index 0000000000000000000000000000000000000000..4d6c3772f3b020a2d5f97d77fc5dc3849215f4ea --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/receipt_51945287.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "e6d7fafff178fd2e78d141fe94d9386c725888749620f3b809e8d4e87adcb8cc", + "elapsed_s": 37, + "failure_sha256": null, + "host": "cn604-12", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51945287", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "0d8f7378daa763fd8ce323bd94154ab6274598b4b2e1d690d5d14a23385f8af9", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:47:09Z" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/submissions.jsonl b/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..8f8e2cd2caf732b078bffc58e4537388074f1ade --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g5/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g5/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_2K/receipts/export_51933476.json"], "job_id": "51945287", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_CONST_2K/fitcoal_g5.json", "request_sha256": "f9f0d2ce2497de716a6ad21208dd8fcf2e0211aca5bd5f0a7be3ccd6f37dc9ab", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [5], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "0d8f7378daa763fd8ce323bd94154ab6274598b4b2e1d690d5d14a23385f8af9", "stage": "v2", "usage_before": {"account_jobs": 148, "bench_cores": 573, "bench_gpus": 2, "bench_jobs": 96, "bench_pending": 6, "never_startable_pending": 0, "throttle_held_not_counted": 5}, "utc": "2026-09-16T12:46:17Z"} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/envlock_check_51945311.json b/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/envlock_check_51945311.json new file mode 100644 index 0000000000000000000000000000000000000000..d2e53928ebd1b713ba7a1e33f401417eb49fb5ca --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/envlock_check_51945311.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn113-35-l", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51945311", + "status": "PASS", + "utc": "20260916T124716Z" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fit_spec.json b/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..7079b51505849b83edc1afad882c5a5a801de805 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_CONST_2K", + "g": 6, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_2K/r00000006/n32" + ], + "rep": 6, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..94337f7aa36e145471619b71aa2e92bdeb8a64a4 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +3163 1509 933 754 568 475 402 390 276 300 306 231 225 242 189 158 171 147 146 164 146 150 123 129 106 125 117 93 102 116 100 88 97 111 100 66 79 79 79 70 57 92 91 77 67 42 58 48 71 41 48 48 47 47 57 62 51 36 72 58 33 46 86 \ No newline at end of file diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..3a4a7567af919a4409e615e3af8fde0171c002bd --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g6/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g6/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 3 -randSeed 6 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..1c14591634679945de1462a20e78bcf41afd8d44 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fitcoal/decoder.out @@ -0,0 +1,16 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 1,994 changeTypes: 0 +maxLogL = -265.97639591726335 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 2,607 changeTypes: 1 +standardTime: 0.009590667015075913 generations: 50.00 N: 1,956 changeTypes: 0 +maxLogL = -259.45495956558966 + +******** Best: ******** +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 1,994 changeTypes: 0 +maxLogL = -265.97639591726335 + +computing time = 24.47 seconds diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fitcoal/output.txt b/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1619d40263973f90e057098cf9634d7bef2b389 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 1994 +4000000 1994 + diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..47de88aebecef4006ba97a94faaf20de764f8f92 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 3 (recommended) +The proportion of truncated or collapsed SFS types: 0.047619047619047616 + diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/receipt_51945311.json b/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/receipt_51945311.json new file mode 100644 index 0000000000000000000000000000000000000000..203c01967ff75b3e287013c2e34a88cf0e060eb4 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/receipt_51945311.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "abe2b07df3376645f34a8787595ce2ecacc14575d6aec9d807d31d3b07ac66b7", + "elapsed_s": 63, + "failure_sha256": null, + "host": "cn113-35-l", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51945311", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "b001eb6885e7f8e24c64fc537677a6a0238348f78fa75365a6c14a9e33dbcf70", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:47:56Z" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/submissions.jsonl b/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..8c2bb9ab12ba3305a3f34b652abfc201825a0853 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g6/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g6/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_2K/receipts/export_51933476.json"], "job_id": "51945311", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_CONST_2K/fitcoal_g6.json", "request_sha256": "a11c9efc91d2c13fe5d51e6bb12655b9e659e9a2d52dad69bb15a9ea9810e5a5", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [6], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "b001eb6885e7f8e24c64fc537677a6a0238348f78fa75365a6c14a9e33dbcf70", "stage": "v2", "usage_before": {"account_jobs": 148, "bench_cores": 573, "bench_gpus": 2, "bench_jobs": 96, "bench_pending": 6, "never_startable_pending": 0, "throttle_held_not_counted": 5}, "utc": "2026-09-16T12:46:30Z"} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/envlock_check_51945314.json b/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/envlock_check_51945314.json new file mode 100644 index 0000000000000000000000000000000000000000..b683e76710b8edc6958387b62ffc3606f65805e5 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/envlock_check_51945314.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-11", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51945314", + "status": "PASS", + "utc": "20260916T124655Z" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fit_spec.json b/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..a929d65d93dbd6d058b533e3ba3ea563ba17ddaf --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_CONST_2K", + "g": 7, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_2K/r00000007/n32" + ], + "rep": 7, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..9b99ae025187a85387515cb281ef0a8841537f4b --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +2938 1557 1081 698 562 509 414 351 346 264 277 227 296 192 214 204 208 173 169 160 159 144 164 153 155 131 113 110 107 100 86 103 115 95 108 91 99 94 84 77 66 67 60 81 79 83 65 72 59 45 58 49 44 35 34 38 66 63 48 41 74 22 51 \ No newline at end of file diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..4c2c1e9aee3837b9ac1eb6c2813b8895218d8f1e --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g7/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g7/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 7 -randSeed 7 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..e0f5949dfcd0891e39235a735fdbcaa4d75f134b --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fitcoal/decoder.out @@ -0,0 +1,16 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 2,033 changeTypes: 0 +maxLogL = -261.78414753901563 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 1,966 changeTypes: 1 +standardTime: 0.29516306137038034 generations: 1160.79 N: 2,105 changeTypes: 0 +maxLogL = -258.0127710756713 + +******** Best: ******** +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 2,033 changeTypes: 0 +maxLogL = -261.78414753901563 + +computing time = 30.59 seconds diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fitcoal/output.txt b/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..9db7a6038e79a0fa9b818366cc4a005b77a117a7 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 2033 +4000000 2033 + diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..60a4026cfed4d2197c27e31e62c392ba7b76cc5f --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 7 (recommended) +The proportion of truncated or collapsed SFS types: 0.1111111111111111 + diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/receipt_51945314.json b/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/receipt_51945314.json new file mode 100644 index 0000000000000000000000000000000000000000..c03b25a8828d1255fa2a4f994cfbd358033d348c --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/receipt_51945314.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "70f5a63eedf4dd0202bc68fc72160e306f52b5b7f60f0582464ebdb6022c8ce4", + "elapsed_s": 42, + "failure_sha256": null, + "host": "cn604-11", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51945314", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "a94ee9dcf36876df25bd23f6a18287d1baf86c7ade60035cadbf84775500e857", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:47:35Z" +} diff --git a/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/submissions.jsonl b/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..b211793f3f30f604452a1cd3c28314c02725ae4b --- /dev/null +++ b/estimates/fitcoal/a1/CONST_2K/K1/g7/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_2K/K1/g7/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_2K/receipts/export_51933476.json"], "job_id": "51945314", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_CONST_2K/fitcoal_g7.json", "request_sha256": "cbfb11088508647dd15b5ff61b2427894b838403f048f9c164bbc78dbd989b55", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [7], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "a94ee9dcf36876df25bd23f6a18287d1baf86c7ade60035cadbf84775500e857", "stage": "v2", "usage_before": {"account_jobs": 145, "bench_cores": 553, "bench_gpus": 2, "bench_jobs": 93, "bench_pending": 7, "never_startable_pending": 0, "throttle_held_not_counted": 5}, "utc": "2026-09-16T12:46:38Z"} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/envlock_check_51947206.json b/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/envlock_check_51947206.json new file mode 100644 index 0000000000000000000000000000000000000000..dd83cf2e9d06626e6804ac933c89a56d0d41bb8a --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/envlock_check_51947206.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-07", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51947206", + "status": "PASS", + "utc": "20260916T125709Z" +} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fit_spec.json b/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..d787d3558e8f95a817fe5163e46658b9de4ef188 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_CONST_50K", + "g": 0, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_50K/r00000000/n32" + ], + "rep": 0, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..c15d48201a07dd607f16d0656a6eb25ccfa7ace3 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +75328 37480 24738 18928 15200 12653 10763 9358 8566 7560 6969 6454 5546 5365 4917 4741 4382 4329 4061 3606 3663 3426 3298 3044 3039 2896 2811 2760 2623 2457 2392 2354 2232 2224 2119 2127 2027 1926 1959 1736 1809 1752 1753 1684 1644 1640 1607 1638 1476 1623 1449 1519 1549 1383 1396 1294 1383 1217 1233 1337 1284 1156 1247 \ No newline at end of file diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..b09221d6a54fd7749aaebcb86b541a40f2424e90 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g0/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g0/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 1 -randSeed 0 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..3855fb41cdc5efde60f5de862c03100b01d6a935 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fitcoal/decoder.out @@ -0,0 +1,16 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 50,206 changeTypes: 0 +maxLogL = -370.52211749636535 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 50,041 changeTypes: 1 +standardTime: 0.08402562063331029 generations: 8409.53 N: 50,269 changeTypes: 0 +maxLogL = -370.20723202928366 + +******** Best: ******** +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 50,206 changeTypes: 0 +maxLogL = -370.52211749636535 + +computing time = 37.03 seconds diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fitcoal/output.txt b/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..6abfb9e28f3bf4ff3fc39e05249f16fba55fdb00 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 50206 +4000000 50206 + diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..5dc872fd79c57a0630616d4dc65b24263eb0d126 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 1 (recommended) +The proportion of truncated or collapsed SFS types: 0.015873015873015872 + diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/receipt_51947206.json b/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/receipt_51947206.json new file mode 100644 index 0000000000000000000000000000000000000000..96d91a1d0f351cdc085398114e123c6bab443958 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/receipt_51947206.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "128b58d9f317428735f8528865528a086d7c2e2c4c231e3957707c41de0d7276", + "elapsed_s": 115, + "failure_sha256": null, + "host": "cn604-07", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51947206", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "2c7788423982b8a98937644f5a2e65b9a2589fa696f55539eb25ec578bed61d2", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:58:06Z" +} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/submissions.jsonl b/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..0843190033d3c3fe3cb5ed6363bcde9983375cb5 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g0/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g0/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_50K/receipts/export_51934599.json"], "job_id": "51947206", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_CONST_50K/fitcoal_g0.json", "request_sha256": "e557bcddd9abb020b3f8887604d507ddc766ac21776bd5d6b56524bb6b5aa5d9", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [0], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "2c7788423982b8a98937644f5a2e65b9a2589fa696f55539eb25ec578bed61d2", "stage": "v2", "usage_before": {"account_jobs": 127, "bench_cores": 487, "bench_gpus": 20, "bench_jobs": 75, "bench_pending": 2, "never_startable_pending": 0, "throttle_held_not_counted": 1}, "utc": "2026-09-16T12:56:07Z"} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/envlock_check_51947235.json b/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/envlock_check_51947235.json new file mode 100644 index 0000000000000000000000000000000000000000..8fdfefe347f264e317b630e144379eb7cfab3598 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/envlock_check_51947235.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn113-35-l", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51947235", + "status": "PASS", + "utc": "20260916T125629Z" +} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fit_spec.json b/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..d2e81536da01f7c28215b61746c076bf80e59aac --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_CONST_50K", + "g": 1, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_50K/r00000001/n32" + ], + "rep": 1, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..faaf8eb60fdc0a64bfd8a5c2a7e32eef2e44dc1d --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +75067 36932 24274 18749 15019 12765 10732 9467 8369 7560 6735 6195 5934 5347 5012 4755 4393 4207 3935 3843 3572 3452 3376 3101 3041 2981 2755 2639 2574 2520 2348 2397 2365 2229 2162 2018 1943 2000 1962 1931 1752 1872 1687 1622 1623 1596 1573 1535 1608 1463 1478 1487 1267 1516 1341 1380 1319 1385 1277 1223 1167 1226 1168 \ No newline at end of file diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..245794ad6a0dba077e95a70a298a5a2cf7ebe1ae --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g1/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g1/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 1 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..30fec93c3050b5dc6a5d89e625ae850a45e1d981 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fitcoal/decoder.out @@ -0,0 +1,16 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 49,944 changeTypes: 0 +maxLogL = -378.05210559944135 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 49,584 changeTypes: 1 +standardTime: 0.16930950184444857 generations: 16790.00 N: 50,182 changeTypes: 0 +maxLogL = -375.18187492120524 + +******** Best: ******** +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 49,944 changeTypes: 0 +maxLogL = -378.05210559944135 + +computing time = 62.97 seconds diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fitcoal/output.txt b/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..9266dec92d7ffa1e00ffe507f5d150ef7cd8f552 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 49944 +4000000 49944 + diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/receipt_51947235.json b/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/receipt_51947235.json new file mode 100644 index 0000000000000000000000000000000000000000..e6c914d1f2b06c32cb1b4d9616ba44348f107bc0 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/receipt_51947235.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "11d74e0783b55a602d7d69dbb34c18e2a18b6e5da92dc2a013daa4517e95f5f9", + "elapsed_s": 83, + "failure_sha256": null, + "host": "cn113-35-l", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51947235", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "b9b872580d5ef16ed4320545224f8ed2c0aa09b543eae530d8647e13d1082d8e", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:57:48Z" +} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/submissions.jsonl b/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..17a8f572d6bf040f252762106c18aef74f3dfb2c --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g1/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g1/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_50K/receipts/export_51934599.json"], "job_id": "51947235", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_CONST_50K/fitcoal_g1.json", "request_sha256": "4e8a5d09899734fe7ecaca15f25659790a3f7c83cc157f5a98155038d8f7ea37", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [1], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "b9b872580d5ef16ed4320545224f8ed2c0aa09b543eae530d8647e13d1082d8e", "stage": "v2", "usage_before": {"account_jobs": 127, "bench_cores": 481, "bench_gpus": 20, "bench_jobs": 75, "bench_pending": 2, "never_startable_pending": 0, "throttle_held_not_counted": 1}, "utc": "2026-09-16T12:56:20Z"} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g2/n32/submissions.jsonl b/estimates/fitcoal/a1/CONST_50K/K1/g2/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..1b35fd35add7656b29c0b75ce6262b02672bad51 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g2/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g2/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_50K/receipts/export_51934599.json"], "job_id": "51947237", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_CONST_50K/fitcoal_g2.json", "request_sha256": "5d1b5f2be4017811e1821f24efd124af74ddb747f567054cf5a143acdd14f0ab", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [2], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "ca5f92299c74b4232edb09a09ae7ef9b2bc2e6d5b995dcd3cf4e3b62f09e2ae1", "stage": "v2", "usage_before": {"account_jobs": 128, "bench_cores": 483, "bench_gpus": 20, "bench_jobs": 76, "bench_pending": 3, "never_startable_pending": 0, "throttle_held_not_counted": 1}, "utc": "2026-09-16T12:56:33Z"} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/envlock_check_51947238.json b/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/envlock_check_51947238.json new file mode 100644 index 0000000000000000000000000000000000000000..a968e1e3314ddedfa83c3a7d84b5118b4dc3ca9f --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/envlock_check_51947238.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-17", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51947238", + "status": "PASS", + "utc": "20260916T130159Z" +} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fit_spec.json b/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..394c9beb587b7ec1599680bb7d69dd1152b103bf --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_CONST_50K", + "g": 3, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_50K/r00000003/n32" + ], + "rep": 3, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..4825f1f3bcee95ba05b9a24b6511baecbfa25858 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +73412 37571 24833 18808 14698 12686 10970 9652 8303 7368 6796 6221 5851 5579 4866 4706 4359 4269 3903 3621 3571 3428 3232 3102 2950 2871 2767 2657 2744 2498 2346 2307 2211 2299 2207 2106 2009 2036 1963 1785 1807 1812 1660 1785 1601 1618 1541 1589 1467 1531 1537 1461 1419 1374 1432 1395 1346 1275 1106 1196 1274 1122 1144 \ No newline at end of file diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..d25531315e30e8385aba5343e81ec633e110b914 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g3/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g3/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 1 -randSeed 3 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..12926190758cdd5f2175c4f30ea97d4fc428f038 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fitcoal/decoder.out @@ -0,0 +1,16 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 49,785 changeTypes: 0 +maxLogL = -389.05967643566146 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 17,146 changeTypes: 2 +standardTime: 0.001565573163075948 generations: 87.46 N: 50,017 changeTypes: 0 +maxLogL = -375.4502120972038 + +******** Best: ******** +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 49,785 changeTypes: 0 +maxLogL = -389.05967643566146 + +computing time = 12.80 seconds diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fitcoal/output.txt b/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..3d026fc7a691afbbe5df20b9a70f3caf503a0d47 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 49785 +4000000 49785 + diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..5dc872fd79c57a0630616d4dc65b24263eb0d126 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 1 (recommended) +The proportion of truncated or collapsed SFS types: 0.015873015873015872 + diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/receipt_51947238.json b/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/receipt_51947238.json new file mode 100644 index 0000000000000000000000000000000000000000..1b17b1199c15b249b434bf450cc83b3f22e07b7f --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/receipt_51947238.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "e46c6c616d8182a28915e9117218541af22f22e20c4e13aada1247c6b1004a70", + "elapsed_s": 283, + "failure_sha256": null, + "host": "cn604-17", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51947238", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "08655f3449f7be1a9b81d2dd6e0d56b86d06f64ebbe07f2d33c433eea08f3dfe", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T13:02:23Z" +} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/submissions.jsonl b/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..b1634133c65cd2266dbbcd461af3a9f0c7b72130 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g3/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g3/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_50K/receipts/export_51934599.json"], "job_id": "51947238", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_CONST_50K/fitcoal_g3.json", "request_sha256": "161eeb17c4ee35dd2382f80f24c1be7c59a1da3233631a3b9afa5ecd3271fcf2", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [3], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "08655f3449f7be1a9b81d2dd6e0d56b86d06f64ebbe07f2d33c433eea08f3dfe", "stage": "v2", "usage_before": {"account_jobs": 129, "bench_cores": 485, "bench_gpus": 20, "bench_jobs": 77, "bench_pending": 3, "never_startable_pending": 0, "throttle_held_not_counted": 1}, "utc": "2026-09-16T12:56:42Z"} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/envlock_check_51947239.json b/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/envlock_check_51947239.json new file mode 100644 index 0000000000000000000000000000000000000000..7be2b014d78fcd8e31a6710da8d227d56ca13051 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/envlock_check_51947239.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-15", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51947239", + "status": "PASS", + "utc": "20260916T130244Z" +} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fit_spec.json b/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..68c722d8cb1f7977acea1fceec4b010acc9e6232 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_CONST_50K", + "g": 4, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_50K/r00000004/n32" + ], + "rep": 4, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..66c1c2222253cdb643859f8186f3a28cc82767ba --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +75504 37044 25244 19270 15007 12522 11035 9568 8235 7450 6811 6147 5783 5527 4763 4894 4445 4229 3881 3862 3574 3432 3427 3209 3027 2758 2824 2562 2570 2444 2343 2265 2232 2159 2197 1899 1995 1987 1832 1893 1871 1785 1750 1759 1702 1645 1607 1587 1522 1545 1598 1455 1404 1424 1402 1488 1350 1285 1281 1320 1166 1282 1236 \ No newline at end of file diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..e5c83f74d701e770e0f4d606c5d80d3c8dda5d9b --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g4/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g4/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 4 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..7583e096a77f1511cf7bb0dbe6edc6b75365ccbd --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fitcoal/decoder.out @@ -0,0 +1,16 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 50,239 changeTypes: 0 +maxLogL = -395.1866154820109 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 50,178 changeTypes: 1 +standardTime: 1.9989998852598132 generations: 200612.04 N: 50,907 changeTypes: 0 +maxLogL = -394.831825076898 + +******** Best: ******** +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 50,239 changeTypes: 0 +maxLogL = -395.1866154820109 + +computing time = 34.95 seconds diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fitcoal/output.txt b/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..cbea5e715362fd77dfa66d240723d94b700ef902 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 50239 +4000000 50239 + diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/receipt_51947239.json b/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/receipt_51947239.json new file mode 100644 index 0000000000000000000000000000000000000000..c81a1139e09e761073c366f3867b93b63f3395a8 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/receipt_51947239.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "cac00710d0d1ea9c2440583e2c52e1ecd04cb197f818ac74524c130dc09a385a", + "elapsed_s": 350, + "failure_sha256": null, + "host": "cn604-15", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51947239", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "a94972ed192c5f0d65341b4bf812c7066906dbee5b0d3c95dfe48996dc161a90", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T13:03:30Z" +} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/submissions.jsonl b/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..b27b3eb52055b5e4bdf98a3006ac02b91d7bbd34 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g4/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g4/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_50K/receipts/export_51934599.json"], "job_id": "51947239", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_CONST_50K/fitcoal_g4.json", "request_sha256": "fa22aaad3352f66163e7eefa168d2d8e378d83bf2e1cf5e1a277d599326fedbf", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [4], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "a94972ed192c5f0d65341b4bf812c7066906dbee5b0d3c95dfe48996dc161a90", "stage": "v2", "usage_before": {"account_jobs": 130, "bench_cores": 487, "bench_gpus": 20, "bench_jobs": 78, "bench_pending": 4, "never_startable_pending": 0, "throttle_held_not_counted": 1}, "utc": "2026-09-16T12:56:51Z"} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/envlock_check_51947240.json b/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/envlock_check_51947240.json new file mode 100644 index 0000000000000000000000000000000000000000..04e915580ce67abf08cf9b2f2939d27dd19e1984 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/envlock_check_51947240.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-15", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51947240", + "status": "PASS", + "utc": "20260916T125810Z" +} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fit_spec.json b/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..2e8907c7fdf25954da5ac4e58b72cad248605269 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_CONST_50K", + "g": 5, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_50K/r00000005/n32" + ], + "rep": 5, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..f4a5fe73ecd2b16a1e391f40a9f526e3feb1b60e --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +73983 37625 24697 18525 15001 12391 10475 9458 8498 7548 6940 6243 5765 5480 5247 4765 4480 4064 4027 3607 3473 3365 3277 3135 2935 2822 2639 2504 2459 2324 2278 2360 2247 2145 2144 1967 2079 1912 1863 1932 1810 1782 1722 1640 1676 1552 1588 1613 1687 1475 1466 1452 1493 1438 1474 1359 1286 1436 1364 1225 1146 1123 1057 \ No newline at end of file diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..a8eadce9fd8c8c5564f4e7f4fcd2256c049b1fec --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g5/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g5/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 5 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..f78d556ec9ed593e9f532de15fcf5df71c924c5d --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fitcoal/decoder.out @@ -0,0 +1,16 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 49,707 changeTypes: 0 +maxLogL = -413.89156168843965 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 24,963 changeTypes: 2 +standardTime: 0.0010016515714961402 generations: 69.26 N: 49,810 changeTypes: 0 +maxLogL = -411.10918382226737 + +******** Best: ******** +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 49,707 changeTypes: 0 +maxLogL = -413.89156168843965 + +computing time = 18.07 seconds diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fitcoal/output.txt b/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b55166a327d06c91df8542f05140431323b7758 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 49707 +4000000 49707 + diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/receipt_51947240.json b/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/receipt_51947240.json new file mode 100644 index 0000000000000000000000000000000000000000..1f5d17fe60903d6a6512d77eae1d2fdb8ad8f2f0 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/receipt_51947240.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "3faf6228fa6ae15ec068431d5f857c4bf96a194eb0afaba505273907fd15a51a", + "elapsed_s": 56, + "failure_sha256": null, + "host": "cn604-15", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51947240", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "ae8edc5110c97ebb7c71ce8f2563819c607da63880d99699e4e0b659a7462753", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:58:36Z" +} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/submissions.jsonl b/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..336cc264bbfe85b421d07feb8769d275c960ca15 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g5/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g5/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_50K/receipts/export_51934599.json"], "job_id": "51947240", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_CONST_50K/fitcoal_g5.json", "request_sha256": "1ae557c80d329e5daa6f93ac1517ded6343500dea585c53e01699c80b5d497c6", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [5], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "ae8edc5110c97ebb7c71ce8f2563819c607da63880d99699e4e0b659a7462753", "stage": "v2", "usage_before": {"account_jobs": 129, "bench_cores": 477, "bench_gpus": 20, "bench_jobs": 77, "bench_pending": 5, "never_startable_pending": 0, "throttle_held_not_counted": 1}, "utc": "2026-09-16T12:56:57Z"} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/envlock_check_51947247.json b/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/envlock_check_51947247.json new file mode 100644 index 0000000000000000000000000000000000000000..036cbcea5135bc0c754c00ff932042629d9a3322 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/envlock_check_51947247.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-15", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51947247", + "status": "PASS", + "utc": "20260916T125818Z" +} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fit_spec.json b/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..2a78f48accd941d297f764585b0b13c3c6ad5b48 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_CONST_50K", + "g": 6, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_50K/r00000006/n32" + ], + "rep": 6, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..dcbef3e1c2a4f9c46c5f5364c51c378df50cb74e --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +75201 37717 24618 18471 15584 12315 10683 9524 8234 7600 6673 6274 5586 5580 4975 4732 4329 4130 4088 3819 3514 3384 3361 3094 2935 2905 2738 2662 2391 2455 2561 2369 2326 2180 2125 2047 1927 1922 1856 1825 1850 1917 1790 1590 1780 1683 1617 1584 1578 1609 1394 1371 1407 1353 1356 1402 1325 1313 1274 1266 1201 1158 1133 \ No newline at end of file diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..91d7d8fbbcf7e40534c42eac4f8c58c37a094121 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g6/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g6/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 6 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..c4d1feed9ea75e308abb60b330630809fe9ce63c --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fitcoal/decoder.out @@ -0,0 +1,16 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 50,006 changeTypes: 0 +maxLogL = -394.8929813609511 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 50,685 changeTypes: 1 +standardTime: 0.011359753586521708 generations: 1151.54 N: 49,958 changeTypes: 0 +maxLogL = -394.4664788604341 + +******** Best: ******** +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 50,006 changeTypes: 0 +maxLogL = -394.8929813609511 + +computing time = 28.36 seconds diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fitcoal/output.txt b/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..2bd1d7b30911aeb6507ee52da45c1f605226dd85 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 50006 +4000000 50006 + diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/receipt_51947247.json b/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/receipt_51947247.json new file mode 100644 index 0000000000000000000000000000000000000000..585cc95a3ca4762b76baa36ac7ac9022a1de3976 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/receipt_51947247.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "45284507af7f5ec8f00836aac1dd3bbe48fcd949238f1701ee9812ededb36267", + "elapsed_s": 75, + "failure_sha256": null, + "host": "cn604-15", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51947247", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "f85ca9c83163cca537c00eecb9d6d04feb048fc255c5feaa894ab21427186c95", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:58:55Z" +} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/submissions.jsonl b/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..46a772d4bfe9bd3247621b5e7216fb37e2bc6674 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g6/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g6/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_50K/receipts/export_51934599.json"], "job_id": "51947247", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_CONST_50K/fitcoal_g6.json", "request_sha256": "1d0cd135dc50d2fa6ffa65bd3f22e11c074478694eb6f54699b1e0d3984789a5", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [6], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "f85ca9c83163cca537c00eecb9d6d04feb048fc255c5feaa894ab21427186c95", "stage": "v2", "usage_before": {"account_jobs": 129, "bench_cores": 475, "bench_gpus": 20, "bench_jobs": 77, "bench_pending": 6, "never_startable_pending": 0, "throttle_held_not_counted": 1}, "utc": "2026-09-16T12:57:17Z"} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/envlock_check_51947250.json b/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/envlock_check_51947250.json new file mode 100644 index 0000000000000000000000000000000000000000..df56f8c4890700aceb38c4f98cf960f5f45e2c0e --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/envlock_check_51947250.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-15", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51947250", + "status": "PASS", + "utc": "20260916T125757Z" +} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fit_spec.json b/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..9ed0c3bf72bc9c57b6b757bdd31a7eee44536d2e --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_CONST_50K", + "g": 7, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_50K/r00000007/n32" + ], + "rep": 7, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..0572fc971e4a74f5fc29bd4de7326212ccdaf01c --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +74327 36035 24689 18008 14554 12207 11051 9604 8094 7398 6640 6121 5723 5188 4955 4703 4228 4084 3791 3640 3476 3214 3180 3086 2962 2804 2710 2604 2581 2428 2428 2251 2271 2144 2103 2140 1898 1919 1990 1902 1801 1702 1692 1567 1681 1581 1552 1561 1624 1500 1490 1396 1416 1485 1233 1431 1375 1238 1224 1264 1207 1262 1169 \ No newline at end of file diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..bd8a02efa4914c90d69969318c6e12843c2e74f9 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g7/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g7/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 7 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..4e1a26528fa18ed72c05c620c3785b8f93c44ec8 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fitcoal/decoder.out @@ -0,0 +1,16 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 49,149 changeTypes: 0 +maxLogL = -400.6211517594684 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 88,825 changeTypes: 2 +standardTime: 0.001000009058345539 generations: 130.08 N: 49,043 changeTypes: 0 +maxLogL = -397.6410249212495 + +******** Best: ******** +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 49,149 changeTypes: 0 +maxLogL = -400.6211517594684 + +computing time = 39.21 seconds diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fitcoal/output.txt b/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..033b0e3c338375e1fc33b65fc343c24f1914bb81 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 49149 +4000000 49149 + diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/receipt_51947250.json b/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/receipt_51947250.json new file mode 100644 index 0000000000000000000000000000000000000000..ea1f71ce625726cfd3a3aca114a04496d290fa95 --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/receipt_51947250.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "f6d7f0ad9fa163d33a139d4315f74fab6e73fc6a1949bffc92e4de5d90ffed24", + "elapsed_s": 68, + "failure_sha256": null, + "host": "cn604-15", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51947250", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "09a529fb137674f11f4e788283e1d275e46f4c04cad88909e242f7a218c1c682", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:58:48Z" +} diff --git a/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/submissions.jsonl b/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..e786848f8e35caea245638535cf4d182f7b6270f --- /dev/null +++ b/estimates/fitcoal/a1/CONST_50K/K1/g7/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_CONST_50K/K1/g7/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_CONST_50K/receipts/export_51934599.json"], "job_id": "51947250", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_CONST_50K/fitcoal_g7.json", "request_sha256": "1480ec75dc3a03534b12c391d44e8efb9356cfc599e51bbc8137614a1be7ed24", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [7], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "09a529fb137674f11f4e788283e1d275e46f4c04cad88909e242f7a218c1c682", "stage": "v2", "usage_before": {"account_jobs": 130, "bench_cores": 477, "bench_gpus": 20, "bench_jobs": 78, "bench_pending": 7, "never_startable_pending": 0, "throttle_held_not_counted": 1}, "utc": "2026-09-16T12:57:27Z"} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/envlock_check_51933715.json b/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/envlock_check_51933715.json new file mode 100644 index 0000000000000000000000000000000000000000..21b7ae13ecfb923092494d9ae744213c973e60f9 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/envlock_check_51933715.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-10", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51933715", + "status": "PASS", + "utc": "20260916T111130Z" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fit_spec.json b/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..cc24f66ab911f4a63b9484e522f732a6fe6aa2a9 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_EMP_CEU", + "g": 0, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CEU/r00000000/n32" + ], + "rep": 0, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..3f9da7007fea4b11bfd12840aefb409b5e9b6519 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +27155 9451 5717 4566 3550 3030 2763 2580 2323 2073 2058 1874 1953 1817 1621 1480 1461 1344 1344 1408 1135 1230 1240 1075 1061 1051 1110 996 904 876 896 884 825 781 768 714 747 684 700 712 677 661 587 590 568 555 566 539 542 584 598 520 524 552 472 563 531 394 518 539 405 448 335 \ No newline at end of file diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..fc95dc134be30c43dec1e13e3ce5dc0daf2937cb --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g0/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g0/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 8 -randSeed 0 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..84a167ec924f456a8359932be2c8d4c72c4b70a4 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 15,455 changeTypes: 0 +maxLogL = -1930.1063413677257 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 421,277 changeTypes: 2 +standardTime: 0.003173745749603727 generations: 324.83 N: 14,726 changeTypes: 0 +maxLogL = -1524.8535965336096 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 50,790 changeTypes: 2 +standardTime: 0.07032474376933719 generations: 2046.76 N: 6,012 changeTypes: 1 +standardTime: 0.23829579835438985 generations: 4066.53 N: 18,258 changeTypes: 0 +maxLogL = -309.3218583856442 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 56,477 changeTypes: 1 +standardTime: 0.004809103947238732 generations: 543.21 N: 13,744 changeTypes: 1 +standardTime: 0.08025732076420773 generations: 2617.08 N: 610 changeTypes: 2 +standardTime: 0.21066239827116584 generations: 3176.06 N: 18,217 changeTypes: 0 +maxLogL = -306.7896472399925 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 50,790 changeTypes: 2 +standardTime: 0.07032474376933719 generations: 2046.76 N: 6,012 changeTypes: 1 +standardTime: 0.23829579835438985 generations: 4066.53 N: 18,258 changeTypes: 0 +maxLogL = -309.3218583856442 + +computing time = 769.59 seconds diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fitcoal/output.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..8efca78c896ca43bf29bd2eabd2a2cde50df8086 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fitcoal/output.txt @@ -0,0 +1,106 @@ +year popSize +2000 6313 +2000 6310 +2001 6306 +2001 6303 +2002 6300 +2002 6297 +2003 6294 +2003 6291 +2004 6288 +2004 6285 +2005 6282 +2005 6279 +2006 6276 +2006 6273 +2007 6270 +2007 6267 +2007 6264 +2008 6261 +2008 6257 +2009 6254 +2009 6251 +2010 6248 +2010 6245 +2011 6242 +2011 6239 +2012 6236 +2012 6233 +2013 6230 +2013 6227 +2014 6224 +2014 6221 +2014 6218 +2015 6215 +2015 6212 +2016 6209 +2016 6206 +2017 6203 +2017 6200 +2018 6197 +2018 6194 +2019 6191 +2019 6188 +2020 6185 +2020 6182 +2021 6179 +2021 6176 +2022 6173 +2022 6170 +2022 6167 +2023 6164 +2023 6161 +2024 6158 +2024 6155 +2025 6152 +2025 6149 +2026 6146 +2026 6143 +2027 6140 +2027 6137 +2028 6134 +2028 6131 +2029 6128 +2029 6125 +2029 6122 +2030 6119 +2030 6116 +2031 6113 +2031 6110 +2032 6107 +2032 6104 +2033 6101 +2033 6098 +2034 6095 +2034 6092 +2035 6089 +2035 6086 +2036 6083 +2036 6080 +2036 6077 +2037 6074 +2037 6071 +2038 6068 +2038 6065 +2039 6062 +2039 6059 +2040 6056 +2040 6053 +2041 6050 +2041 6048 +2042 6045 +2042 6042 +2043 6039 +2043 6036 +2043 6033 +2044 6030 +2044 6027 +2045 6024 +2045 6021 +2046 6018 +2046 6015 +2047 6012 +4067 6012 +4067 18258 +4000000 18258 + diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..b2af6ae547b2ec676a99861a16fcc745fe2f79bf --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 8 (recommended) +The proportion of truncated or collapsed SFS types: 0.12698412698412698 + diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/receipt_51933715.json b/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/receipt_51933715.json new file mode 100644 index 0000000000000000000000000000000000000000..bb3223ed2a02e0263b3b3cdd2a74d02791d9843d --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/receipt_51933715.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "9a14955ce9a5643482b8c0cec6d82a94673ce5d4948e246202681fc291a7f928", + "elapsed_s": 807, + "failure_sha256": null, + "host": "cn604-10", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51933715", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "2cb265ea9f4cdf76698b4e0f80c72d662677629a097fd40a2228f7381eacd40d", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:24:29Z" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/submissions.jsonl b/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..fd4bae3bd8ba9d6eeb06a26e49c1cba97ca4f6c5 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g0/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g0/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CEU/receipts/export_51933094.json"], "job_id": "51933715", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_EMP_CEU/fitcoal_g0.json", "request_sha256": "41d72a3e148e5c264e0b72df866249b01f4f312c32c49ab1c2e0c631af1b5060", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [0], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "2cb265ea9f4cdf76698b4e0f80c72d662677629a097fd40a2228f7381eacd40d", "stage": "v2", "usage_before": {"account_jobs": 146, "bench_cores": 404, "bench_gpus": 16, "bench_jobs": 75, "bench_pending": 13, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:10:59Z"} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/envlock_check_51933717.json b/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/envlock_check_51933717.json new file mode 100644 index 0000000000000000000000000000000000000000..1c7a5b85faf215222416b84cce4b57317cb0787c --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/envlock_check_51933717.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-10", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51933717", + "status": "PASS", + "utc": "20260916T111122Z" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fit_spec.json b/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..60e1da318a4bf82a0c467454fb4b08afcf46bc15 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_EMP_CEU", + "g": 1, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CEU/r00000001/n32" + ], + "rep": 1, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..d8f18ddbe397ef30965dbb980b79c169be1df570 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +26350 9218 5606 4150 3430 2963 2730 2558 2433 2021 2036 1919 1703 1713 1590 1497 1468 1378 1304 1250 1232 1127 1154 1239 1105 1109 1034 945 864 840 946 742 854 752 773 758 761 749 745 714 660 624 614 620 569 590 596 564 544 515 500 497 522 460 572 575 512 381 530 495 435 483 356 \ No newline at end of file diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..3ae9e27305aaec3cda61e6583b0ba44348a318e1 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g1/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g1/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 9 -randSeed 1 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..87669905a28d1a3ddb3e4d820a15c9cfb95ddf44 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 15,100 changeTypes: 0 +maxLogL = -1987.9593797905663 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 13,934 changeTypes: 1 +standardTime: 1.9989999650228827 generations: 55709.47 N: 29,668 changeTypes: 0 +maxLogL = -1598.733794039421 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 48,046 changeTypes: 2 +standardTime: 0.10279812162302979 generations: 2357.98 N: 4,339 changeTypes: 1 +standardTime: 0.2263152215116454 generations: 3429.86 N: 18,075 changeTypes: 0 +maxLogL = -296.1265318034875 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 33,902 changeTypes: 1 +standardTime: 0.017108722754647587 generations: 1160.04 N: 6,558 changeTypes: 2 +standardTime: 0.5717738884923331 generations: 14082.59 N: 23,702 changeTypes: 1 +standardTime: 1.8102358422513094 generations: 72790.76 N: 8,105 changeTypes: 0 +maxLogL = -292.8821695890747 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 48,046 changeTypes: 2 +standardTime: 0.10279812162302979 generations: 2357.98 N: 4,339 changeTypes: 1 +standardTime: 0.2263152215116454 generations: 3429.86 N: 18,075 changeTypes: 0 +maxLogL = -296.1265318034875 + +computing time = 795.08 seconds diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fitcoal/output.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..c4efa99d3edbc98c50f9e38cae61b1e668fb699b --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fitcoal/output.txt @@ -0,0 +1,106 @@ +year popSize +2000 6251 +2004 6228 +2007 6205 +2011 6183 +2014 6160 +2018 6138 +2021 6115 +2025 6093 +2029 6071 +2032 6049 +2036 6027 +2039 6005 +2043 5983 +2047 5961 +2050 5939 +2054 5918 +2057 5896 +2061 5875 +2064 5853 +2068 5832 +2072 5811 +2075 5789 +2079 5768 +2082 5747 +2086 5726 +2089 5705 +2093 5685 +2097 5664 +2100 5643 +2104 5623 +2107 5602 +2111 5582 +2115 5562 +2118 5541 +2122 5521 +2125 5501 +2129 5481 +2132 5461 +2136 5441 +2140 5421 +2143 5401 +2147 5382 +2150 5362 +2154 5343 +2158 5323 +2161 5304 +2165 5284 +2168 5265 +2172 5246 +2175 5227 +2179 5208 +2183 5189 +2186 5170 +2190 5151 +2193 5132 +2197 5114 +2200 5095 +2204 5076 +2208 5058 +2211 5040 +2215 5021 +2218 5003 +2222 4985 +2226 4966 +2229 4948 +2233 4930 +2236 4912 +2240 4894 +2243 4877 +2247 4859 +2251 4841 +2254 4824 +2258 4806 +2261 4788 +2265 4771 +2268 4754 +2272 4736 +2276 4719 +2279 4702 +2283 4685 +2286 4668 +2290 4651 +2294 4634 +2297 4617 +2301 4600 +2304 4583 +2308 4567 +2311 4550 +2315 4533 +2319 4517 +2322 4500 +2326 4484 +2329 4468 +2333 4451 +2336 4435 +2340 4419 +2344 4403 +2347 4387 +2351 4371 +2354 4355 +2358 4339 +3430 4339 +3430 18075 +4000000 18075 + diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..015390263a90901dc3f7155b422a959bcbc7f873 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 9 (recommended) +The proportion of truncated or collapsed SFS types: 0.14285714285714285 + diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/receipt_51933717.json b/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/receipt_51933717.json new file mode 100644 index 0000000000000000000000000000000000000000..6765245aaaf765f37978dee113dffbf34f410fca --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/receipt_51933717.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "dea5eb0581ee39ac247b41c827526f26bee3b40499a13c42dec424a40fe9af98", + "elapsed_s": 818, + "failure_sha256": null, + "host": "cn604-10", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51933717", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "81ecc2ea02eeb383c0b57539599862d2ad452ae997e40ef7aafad19717dc7352", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:24:51Z" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/submissions.jsonl b/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..bd57d8ea5641b094ddcdb08d294dd3ae6e7d9c96 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g1/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g1/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CEU/receipts/export_51933094.json"], "job_id": "51933717", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_EMP_CEU/fitcoal_g1.json", "request_sha256": "43ca6dd1ebabe236d4347026d32aefe8a09d4aa62742dc64deae2569ad53d9e0", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [1], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "81ecc2ea02eeb383c0b57539599862d2ad452ae997e40ef7aafad19717dc7352", "stage": "v2", "usage_before": {"account_jobs": 147, "bench_cores": 406, "bench_gpus": 16, "bench_jobs": 76, "bench_pending": 13, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:11:10Z"} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/envlock_check_51933718.json b/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/envlock_check_51933718.json new file mode 100644 index 0000000000000000000000000000000000000000..5f9e9280693facc05e554be2f1a327ce82453d8c --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/envlock_check_51933718.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-04", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51933718", + "status": "PASS", + "utc": "20260916T111133Z" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fit_spec.json b/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..89b1268cccdc7409cebcbc8d2fcd0f602a7e1c07 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_EMP_CEU", + "g": 2, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CEU/r00000002/n32" + ], + "rep": 2, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..b58a6fe5302588cad7923f40fb532203ca16f19e --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +26584 9018 6097 4365 3548 3034 2534 2459 2278 2056 2105 1875 1863 1834 1730 1626 1466 1501 1406 1275 1265 1138 1100 1119 1036 1008 885 950 967 830 906 848 869 784 827 791 703 737 642 691 736 676 658 656 609 674 630 607 592 593 542 538 524 434 535 427 432 392 470 384 478 393 354 \ No newline at end of file diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..f479000025e0404e2ac9e98e02df254347fc8cb8 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g2/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g2/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 3 -randSeed 2 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..075972afe975b058eeaa7ceaab7f5f28344fd881 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 15,365 changeTypes: 0 +maxLogL = -2057.949380194088 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 14,130 changeTypes: 1 +standardTime: 1.5432432924693356 generations: 43611.72 N: 23,863 changeTypes: 0 +maxLogL = -1627.3728847605917 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 46,159 changeTypes: 2 +standardTime: 0.09938191295450352 generations: 2376.23 N: 4,700 changeTypes: 1 +standardTime: 0.2297487344342172 generations: 3601.75 N: 18,317 changeTypes: 0 +maxLogL = -382.10350240074195 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 81,835 changeTypes: 1 +standardTime: 0.0026285017466640462 generations: 430.21 N: 13,675 changeTypes: 1 +standardTime: 0.08697458225013462 generations: 2737.06 N: 227 changeTypes: 2 +standardTime: 0.21511669984797252 generations: 2996.29 N: 18,367 changeTypes: 0 +maxLogL = -367.33163645860236 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 46,159 changeTypes: 2 +standardTime: 0.09938191295450352 generations: 2376.23 N: 4,700 changeTypes: 1 +standardTime: 0.2297487344342172 generations: 3601.75 N: 18,317 changeTypes: 0 +maxLogL = -382.10350240074195 + +computing time = 739.88 seconds diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fitcoal/output.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..607f9c83643792022dd1fc5a3b409f571f8275ad --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fitcoal/output.txt @@ -0,0 +1,106 @@ +year popSize +2000 6749 +2004 6724 +2008 6700 +2011 6676 +2015 6652 +2019 6628 +2023 6604 +2026 6580 +2030 6556 +2034 6532 +2038 6509 +2041 6485 +2045 6462 +2049 6439 +2053 6415 +2056 6392 +2060 6369 +2064 6346 +2068 6323 +2071 6300 +2075 6278 +2079 6255 +2083 6232 +2087 6210 +2090 6187 +2094 6165 +2098 6143 +2102 6121 +2105 6099 +2109 6077 +2113 6055 +2117 6033 +2120 6011 +2124 5989 +2128 5968 +2132 5946 +2135 5925 +2139 5903 +2143 5882 +2147 5861 +2150 5840 +2154 5818 +2158 5797 +2162 5776 +2166 5756 +2169 5735 +2173 5714 +2177 5694 +2181 5673 +2184 5652 +2188 5632 +2192 5612 +2196 5591 +2199 5571 +2203 5551 +2207 5531 +2211 5511 +2214 5491 +2218 5471 +2222 5452 +2226 5432 +2230 5412 +2233 5393 +2237 5373 +2241 5354 +2245 5335 +2248 5315 +2252 5296 +2256 5277 +2260 5258 +2263 5239 +2267 5220 +2271 5201 +2275 5182 +2278 5164 +2282 5145 +2286 5127 +2290 5108 +2293 5090 +2297 5071 +2301 5053 +2305 5035 +2309 5016 +2312 4998 +2316 4980 +2320 4962 +2324 4944 +2327 4927 +2331 4909 +2335 4891 +2339 4873 +2342 4856 +2346 4838 +2350 4821 +2354 4803 +2357 4786 +2361 4769 +2365 4752 +2369 4734 +2372 4717 +2376 4700 +3602 4700 +3602 18317 +4000000 18317 + diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..47de88aebecef4006ba97a94faaf20de764f8f92 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 3 (recommended) +The proportion of truncated or collapsed SFS types: 0.047619047619047616 + diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/receipt_51933718.json b/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/receipt_51933718.json new file mode 100644 index 0000000000000000000000000000000000000000..139df2fddbc343b0323cc09bf9fdb32fd7fec776 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/receipt_51933718.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "77b07d76196984261217a5f8ecb44f9eb64d6666abc0b632edb27a18d99ab265", + "elapsed_s": 772, + "failure_sha256": null, + "host": "cn604-04", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51933718", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "f7c539e9055a8ee46d525c2fe97a8cc7eea73d283dc41ce58ef282dd9a9fac6a", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:24:08Z" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/submissions.jsonl b/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..93e1b8ec7a4b3e724ae451c08eddc4b736a8cfc7 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g2/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g2/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CEU/receipts/export_51933094.json"], "job_id": "51933718", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_EMP_CEU/fitcoal_g2.json", "request_sha256": "065c5f585c2885bc284744cceddeda658e75329392159023194a7e0fd78ca3e6", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [2], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "f7c539e9055a8ee46d525c2fe97a8cc7eea73d283dc41ce58ef282dd9a9fac6a", "stage": "v2", "usage_before": {"account_jobs": 148, "bench_cores": 408, "bench_gpus": 16, "bench_jobs": 77, "bench_pending": 13, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:11:14Z"} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/envlock_check_51933719.json b/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/envlock_check_51933719.json new file mode 100644 index 0000000000000000000000000000000000000000..2d43727a603d69680846f6cd6b316d6160d5179a --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/envlock_check_51933719.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-14", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51933719", + "status": "PASS", + "utc": "20260916T111129Z" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fit_spec.json b/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..a20340df73c231b07954529785aea74890742636 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_EMP_CEU", + "g": 3, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CEU/r00000003/n32" + ], + "rep": 3, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..3f408e3dcf28d21153fe5aa8afdee1f85bbefb9b --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +27096 9600 5856 4585 3719 3376 2912 2520 2413 2258 2021 1976 1862 1753 1685 1541 1453 1505 1470 1257 1298 1299 1162 1113 1036 1051 990 1086 983 972 908 874 966 908 838 772 731 715 699 659 649 679 683 626 664 661 540 539 542 531 543 471 489 585 524 506 586 448 540 482 418 513 454 \ No newline at end of file diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..b45896040560966b8ef816acd06cacc0cbe0e231 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g3/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g3/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 3 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..3a86a753ac1d33d372672e032247c1d578424cbe --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 15,875 changeTypes: 0 +maxLogL = -1981.8970583203054 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 14,583 changeTypes: 1 +standardTime: 1.6844926847887918 generations: 49130.24 N: 25,904 changeTypes: 0 +maxLogL = -1507.6264756723654 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 56,503 changeTypes: 2 +standardTime: 0.04150265384825307 generations: 1523.51 N: 8,092 changeTypes: 1 +standardTime: 0.28230608107412586 generations: 5420.53 N: 18,988 changeTypes: 0 +maxLogL = -361.54591087148856 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 43,566 changeTypes: 1 +standardTime: 0.008992004848965361 generations: 783.49 N: 10,254 changeTypes: 1 +standardTime: 0.14302456805448727 generations: 3532.20 N: 239 changeTypes: 2 +standardTime: 0.23369040468670493 generations: 3724.17 N: 18,941 changeTypes: 0 +maxLogL = -360.12491958764394 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 56,503 changeTypes: 2 +standardTime: 0.04150265384825307 generations: 1523.51 N: 8,092 changeTypes: 1 +standardTime: 0.28230608107412586 generations: 5420.53 N: 18,988 changeTypes: 0 +maxLogL = -361.54591087148856 + +computing time = 582.90 seconds diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fitcoal/output.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..19335411281e1820ae6ec107aa195aa05f31abed --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 8092 +5421 8092 +5421 18988 +4000000 18988 + diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/receipt_51933719.json b/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/receipt_51933719.json new file mode 100644 index 0000000000000000000000000000000000000000..2495dfb572a6f48fecadd1cb49484d51d0aeb476 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/receipt_51933719.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "272cfec9d2aa6e40f734c3a0155ee4c3fbe4ea5f5e99fe093e632a6c7fd2868b", + "elapsed_s": 600, + "failure_sha256": null, + "host": "cn604-14", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51933719", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "7823d44fc202d24c08e55866ed02b37a6f3ff33cd20db3e70ae7c85b8290105f", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:21:23Z" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/submissions.jsonl b/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..3c3e2145d8a8424ba49acbe16d115262edbe1ab4 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g3/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g3/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CEU/receipts/export_51933094.json"], "job_id": "51933719", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_EMP_CEU/fitcoal_g3.json", "request_sha256": "ff0596b1e97d4520af6d64ea8aac1942e436b9b942d8c82ec15ecb156e9a61d2", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [3], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "7823d44fc202d24c08e55866ed02b37a6f3ff33cd20db3e70ae7c85b8290105f", "stage": "v2", "usage_before": {"account_jobs": 149, "bench_cores": 410, "bench_gpus": 16, "bench_jobs": 78, "bench_pending": 13, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:11:18Z"} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/envlock_check_51933720.json b/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/envlock_check_51933720.json new file mode 100644 index 0000000000000000000000000000000000000000..d997d26aca4040e486a537b0eee2f9a8f4af0520 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/envlock_check_51933720.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-17", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51933720", + "status": "PASS", + "utc": "20260916T111141Z" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fit_spec.json b/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..80b7898547ebd8d860b84b8e7705fb28be956748 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_EMP_CEU", + "g": 4, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CEU/r00000004/n32" + ], + "rep": 4, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..a5e64f2cf1ef911c3aaa1a723c3766724443d9a3 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +26445 9290 5937 4624 3571 3227 2654 2546 2389 2142 2012 1936 1764 1589 1711 1497 1437 1486 1416 1255 1175 1222 1249 1174 1095 1029 988 974 947 958 954 779 970 858 788 667 781 715 690 643 657 695 603 704 635 621 562 555 530 452 553 459 588 503 499 454 468 498 445 553 415 494 427 \ No newline at end of file diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..3dd1b419ba590c1c72a4968f75ba5d575dbf6e29 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g4/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g4/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 4 -randSeed 4 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..51ffcec174138238cc7a0b26d75cc09639b7c4f4 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 15,449 changeTypes: 0 +maxLogL = -1867.6394009642731 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 14,246 changeTypes: 1 +standardTime: 1.7034537526450564 generations: 48533.41 N: 25,530 changeTypes: 0 +maxLogL = -1456.0414048693751 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 52,879 changeTypes: 2 +standardTime: 0.041807653918755315 generations: 1498.56 N: 8,084 changeTypes: 1 +standardTime: 0.28989161605140806 generations: 5509.36 N: 18,521 changeTypes: 0 +maxLogL = -360.2641547420635 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 59,209 changeTypes: 2 +standardTime: 0.030998899723545324 generations: 1251.70 N: 9,136 changeTypes: 1 +standardTime: 0.6080832866540703 generations: 11796.54 N: 159,554 changeTypes: 2 +standardTime: 0.8424528622904741 generations: 31099.16 N: 16,163 changeTypes: 0 +maxLogL = -351.67313227220257 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 52,879 changeTypes: 2 +standardTime: 0.041807653918755315 generations: 1498.56 N: 8,084 changeTypes: 1 +standardTime: 0.28989161605140806 generations: 5509.36 N: 18,521 changeTypes: 0 +maxLogL = -360.2641547420635 + +computing time = 672.03 seconds diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fitcoal/output.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..c3c3c39bd526dc8014d23b558719aafb921984da --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 8084 +5509 8084 +5509 18521 +4000000 18521 + diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..f17274d89d9d62d06ab72eba6a878b5eb095d46b --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 4 (recommended) +The proportion of truncated or collapsed SFS types: 0.06349206349206349 + diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/receipt_51933720.json b/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/receipt_51933720.json new file mode 100644 index 0000000000000000000000000000000000000000..a5d1106552ab3dc9bef7915d7d8601136c6654de --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/receipt_51933720.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "58e2010af7f094df71072ac4d19945d8ab2f422fe85b62100bfba9e5a853c843", + "elapsed_s": 687, + "failure_sha256": null, + "host": "cn604-17", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51933720", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "c303f29d0aad792620fa95f8700adc8c7dbb2110055d0e78c4e7e72fcf2f1a01", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:23:06Z" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/submissions.jsonl b/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..793ea4a33cc1baca3775e996c8bbb862067bcf48 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g4/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g4/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CEU/receipts/export_51933094.json"], "job_id": "51933720", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_EMP_CEU/fitcoal_g4.json", "request_sha256": "64416e3735271e5f6289105b1dfade9fd6d5e03a2c732ff301916579ade1627f", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [4], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "c303f29d0aad792620fa95f8700adc8c7dbb2110055d0e78c4e7e72fcf2f1a01", "stage": "v2", "usage_before": {"account_jobs": 150, "bench_cores": 412, "bench_gpus": 16, "bench_jobs": 79, "bench_pending": 13, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:11:36Z"} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/envlock_check_51933724.json b/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/envlock_check_51933724.json new file mode 100644 index 0000000000000000000000000000000000000000..09c60607f553240c0714722bb6e1a7deb1cdb9b0 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/envlock_check_51933724.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-03", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51933724", + "status": "PASS", + "utc": "20260916T111203Z" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fit_spec.json b/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..3ed0301fa8ba79ff03d5d2f7727b0b440518de54 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_EMP_CEU", + "g": 5, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CEU/r00000005/n32" + ], + "rep": 5, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..d86bb4a964605cdab10a0171089c09bc3f39e08c --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +26738 9491 5843 4278 3543 2912 2844 2491 2234 2222 1949 1809 1854 1811 1568 1420 1312 1388 1291 1300 1148 1135 1167 1171 1116 1087 1039 931 913 882 929 930 899 818 797 724 774 795 731 763 718 601 614 686 644 522 522 558 548 582 533 443 529 537 504 496 511 466 497 485 380 439 425 \ No newline at end of file diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..97ff4033a7bd4a728ac0f66f10766868f99b3b4c --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g5/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g5/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 5 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..21bb5e697c13f8c13c1abcf655a41023248af58f --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 15,409 changeTypes: 0 +maxLogL = -2084.5579877964556 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 14,190 changeTypes: 1 +standardTime: 1.9989999904095839 generations: 56733.44 N: 28,817 changeTypes: 0 +maxLogL = -1636.1616409177777 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 46,380 changeTypes: 2 +standardTime: 0.06352336380588108 generations: 1969.86 N: 6,942 changeTypes: 1 +standardTime: 0.2923691534815218 generations: 5146.98 N: 18,581 changeTypes: 0 +maxLogL = -370.8962673832418 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 49,675 changeTypes: 2 +standardTime: 0.04613922597743438 generations: 1640.39 N: 8,261 changeTypes: 1 +standardTime: 0.5425575428287814 generations: 9842.58 N: 56,992 changeTypes: 1 +standardTime: 0.6436632426101543 generations: 21367.11 N: 17,373 changeTypes: 0 +maxLogL = -366.5735854023533 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 46,380 changeTypes: 2 +standardTime: 0.06352336380588108 generations: 1969.86 N: 6,942 changeTypes: 1 +standardTime: 0.2923691534815218 generations: 5146.98 N: 18,581 changeTypes: 0 +maxLogL = -370.8962673832418 + +computing time = 610.91 seconds diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fitcoal/output.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..ff2a9eb94f26475dd9224bcabb4350662c78c196 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 6942 +5147 6942 +5147 18581 +4000000 18581 + diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/receipt_51933724.json b/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/receipt_51933724.json new file mode 100644 index 0000000000000000000000000000000000000000..8b3f7c181dd3c4e5716b21858b4c60121a37bbc8 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/receipt_51933724.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "9604b4d26a571fdd95a85f18ee6e45455c44b6964e1b29364532941d50b63159", + "elapsed_s": 632, + "failure_sha256": null, + "host": "cn604-03", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51933724", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "5f3394c8f26aba52fbc30366dd231614412718c45ffb04c0fafd7cdc46fa2709", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:22:21Z" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/submissions.jsonl b/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..02494380d6842314c18dff3bab872f89c91b3e68 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g5/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g5/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CEU/receipts/export_51933094.json"], "job_id": "51933724", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_EMP_CEU/fitcoal_g5.json", "request_sha256": "366b7d4de2919d1b8ebb53483f0a2a3d22e82293dfc36e5bc682a2c0e9ca22a6", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [5], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "5f3394c8f26aba52fbc30366dd231614412718c45ffb04c0fafd7cdc46fa2709", "stage": "v2", "usage_before": {"account_jobs": 151, "bench_cores": 414, "bench_gpus": 16, "bench_jobs": 80, "bench_pending": 13, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:11:45Z"} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/envlock_check_51933725.json b/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/envlock_check_51933725.json new file mode 100644 index 0000000000000000000000000000000000000000..cb2a4c62cf5c3b5b7116e673f2a8993a1a4177b0 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/envlock_check_51933725.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn511-18", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51933725", + "status": "PASS", + "utc": "20260916T111234Z" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fit_spec.json b/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..5c204e624ec53cc0291fdbd6e05c422bfab4d6cc --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_EMP_CEU", + "g": 6, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CEU/r00000006/n32" + ], + "rep": 6, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..81b74714876b0f258d8c9cafb600a16850df18ad --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +26420 9521 5859 4326 3684 3003 2725 2527 2266 2160 1982 1923 1663 1725 1515 1623 1537 1635 1448 1301 1241 1233 1251 1063 1091 953 1018 1082 904 1046 789 782 758 835 767 787 832 700 741 734 663 687 684 627 638 613 552 596 559 516 454 531 424 532 520 546 566 436 510 464 467 449 416 \ No newline at end of file diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..748fbf6496b90628701892b4ef40983c389d035b --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g6/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g6/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 6 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..98545323a4fee0a78dc8406ccb20765ecab04179 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 15,495 changeTypes: 0 +maxLogL = -2065.569840584201 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 14,179 changeTypes: 1 +standardTime: 1.563826413797324 generations: 44347.63 N: 24,403 changeTypes: 0 +maxLogL = -1569.3028626670175 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 40,997 changeTypes: 2 +standardTime: 0.21535591564153816 generations: 3362.10 N: 2,672 changeTypes: 1 +standardTime: 0.23160463192587394 generations: 3448.94 N: 18,599 changeTypes: 0 +maxLogL = -395.78512122762095 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 267,473 changeTypes: 2 +standardTime: 0.004164469257082087 generations: 398.64 N: 15,968 changeTypes: 1 +standardTime: 0.07516778007682731 generations: 2666.18 N: 294 changeTypes: 2 +standardTime: 0.21834662189598059 generations: 3021.04 N: 18,588 changeTypes: 0 +maxLogL = -393.1035183351655 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 40,997 changeTypes: 2 +standardTime: 0.21535591564153816 generations: 3362.10 N: 2,672 changeTypes: 1 +standardTime: 0.23160463192587394 generations: 3448.94 N: 18,599 changeTypes: 0 +maxLogL = -395.78512122762095 + +computing time = 602.26 seconds diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fitcoal/output.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..c7b515fbd951b253afd3f74b2f7ac6e1d297ebe5 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fitcoal/output.txt @@ -0,0 +1,106 @@ +year popSize +2000 8078 +2014 7990 +2027 7902 +2041 7815 +2054 7729 +2068 7644 +2082 7560 +2095 7477 +2109 7394 +2123 7313 +2136 7232 +2150 7153 +2163 7074 +2177 6996 +2191 6919 +2204 6843 +2218 6768 +2232 6694 +2245 6620 +2259 6547 +2272 6475 +2286 6404 +2300 6333 +2313 6264 +2327 6195 +2341 6127 +2354 6059 +2368 5993 +2381 5927 +2395 5861 +2409 5797 +2422 5733 +2436 5670 +2449 5608 +2463 5546 +2477 5485 +2490 5425 +2504 5365 +2518 5306 +2531 5248 +2545 5190 +2558 5133 +2572 5076 +2586 5021 +2599 4965 +2613 4911 +2627 4857 +2640 4803 +2654 4750 +2667 4698 +2681 4646 +2695 4595 +2708 4545 +2722 4495 +2736 4445 +2749 4396 +2763 4348 +2776 4300 +2790 4253 +2804 4206 +2817 4160 +2831 4114 +2844 4069 +2858 4024 +2872 3980 +2885 3936 +2899 3893 +2913 3850 +2926 3808 +2940 3766 +2953 3724 +2967 3683 +2981 3643 +2994 3603 +3008 3563 +3022 3524 +3035 3485 +3049 3447 +3062 3409 +3076 3371 +3090 3334 +3103 3298 +3117 3261 +3131 3225 +3144 3190 +3158 3155 +3171 3120 +3185 3086 +3199 3052 +3212 3018 +3226 2985 +3240 2952 +3253 2920 +3267 2888 +3280 2856 +3294 2824 +3308 2793 +3321 2763 +3335 2732 +3348 2702 +3362 2672 +3449 2672 +3449 18599 +4000000 18599 + diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/receipt_51933725.json b/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/receipt_51933725.json new file mode 100644 index 0000000000000000000000000000000000000000..deae3ae08d21a167bef17d63e509157b0d7d85a3 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/receipt_51933725.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "fef9f1a77ebd51c5f56b538148c69b4d1795e34b89333e09df767f478a7105a0", + "elapsed_s": 655, + "failure_sha256": null, + "host": "cn511-18", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51933725", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "da7c3315bcf5fe26d51712491ea514c86d8335d775e44b909248b6a51e468566", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:22:47Z" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/submissions.jsonl b/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..24588bd7647895f69b27d247c5c983f2c59adefc --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g6/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g6/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CEU/receipts/export_51933094.json"], "job_id": "51933725", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_EMP_CEU/fitcoal_g6.json", "request_sha256": "cacd48adcd0cd82896f310145bec0e336f00e9f6f309804385b391593f6fbb7f", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [6], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "da7c3315bcf5fe26d51712491ea514c86d8335d775e44b909248b6a51e468566", "stage": "v2", "usage_before": {"account_jobs": 152, "bench_cores": 416, "bench_gpus": 16, "bench_jobs": 81, "bench_pending": 14, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:11:49Z"} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/envlock_check_51933726.json b/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/envlock_check_51933726.json new file mode 100644 index 0000000000000000000000000000000000000000..553616371dcb9b517a3b0f7cf046bb6ee0b4189e --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/envlock_check_51933726.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-03", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51933726", + "status": "PASS", + "utc": "20260916T111157Z" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fit_spec.json b/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..6ac159a93e0f7597be2d03624ddb59534b839883 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_EMP_CEU", + "g": 7, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CEU/r00000007/n32" + ], + "rep": 7, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..4cdd094b75ff7c053defc30d0a8e04c5006eaa66 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +27027 9289 5831 4372 3557 3284 2711 2522 2301 2024 1909 1927 1802 1599 1549 1506 1623 1390 1274 1227 1222 1161 1059 1099 1105 1136 1064 937 946 902 929 774 799 783 882 757 793 779 769 743 617 671 666 554 577 680 614 549 541 556 561 574 501 519 496 529 491 593 509 458 455 444 452 \ No newline at end of file diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..bc1ed1f5d28d0f7ce835919dd674f036e2cc4b6d --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g7/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g7/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 7 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..eda4c5d8e79eebbfd0f422f9e6ef85d576992f20 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 15,505 changeTypes: 0 +maxLogL = -2145.4653483174684 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 14,217 changeTypes: 1 +standardTime: 1.9989999795285565 generations: 56839.44 N: 29,682 changeTypes: 0 +maxLogL = -1643.946234167795 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 65,770 changeTypes: 2 +standardTime: 0.031678577273575016 generations: 1300.40 N: 8,859 changeTypes: 1 +standardTime: 0.3700710604668399 generations: 7296.26 N: 19,036 changeTypes: 0 +maxLogL = -364.88530523527015 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 49,554 changeTypes: 1 +standardTime: 0.0071682808843394185 generations: 710.43 N: 10,483 changeTypes: 1 +standardTime: 0.15464089697826897 generations: 3802.30 N: 3,857 changeTypes: 1 +standardTime: 0.2982086862429912 generations: 4909.67 N: 18,923 changeTypes: 0 +maxLogL = -364.00159124035645 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 65,770 changeTypes: 2 +standardTime: 0.031678577273575016 generations: 1300.40 N: 8,859 changeTypes: 1 +standardTime: 0.3700710604668399 generations: 7296.26 N: 19,036 changeTypes: 0 +maxLogL = -364.88530523527015 + +computing time = 600.42 seconds diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fitcoal/output.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..1ce20dd6da51bfba7e47275419fbe8a578a7f35e --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 8859 +7296 8859 +7296 19036 +4000000 19036 + diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/receipt_51933726.json b/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/receipt_51933726.json new file mode 100644 index 0000000000000000000000000000000000000000..3213545ba0bdd40d4918899758138f0a067a43a4 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/receipt_51933726.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "0c36cd7b6da110f5d40f62748fc801ea17934058debab825549fe446f2d2bcea", + "elapsed_s": 613, + "failure_sha256": null, + "host": "cn604-03", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51933726", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "da16e64c15a946e89a63d2f5054efe4d14d0a20dcc806e626c41954eb3bcbae8", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:22:08Z" +} diff --git a/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/submissions.jsonl b/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..2105cd7edc0096061127974b091163e316ee13b0 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CEU/K1/g7/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CEU/K1/g7/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CEU/receipts/export_51933094.json"], "job_id": "51933726", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_EMP_CEU/fitcoal_g7.json", "request_sha256": "4c2888bc986aefc770c9dd80089fbdae81a04f1d6f7b08673d6170b511193f1a", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [7], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "da16e64c15a946e89a63d2f5054efe4d14d0a20dcc806e626c41954eb3bcbae8", "stage": "v2", "usage_before": {"account_jobs": 153, "bench_cores": 418, "bench_gpus": 16, "bench_jobs": 82, "bench_pending": 13, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:11:53Z"} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/envlock_check_51933764.json b/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/envlock_check_51933764.json new file mode 100644 index 0000000000000000000000000000000000000000..a16e5c006ccd82ba22d60507790c0e4de542a938 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/envlock_check_51933764.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-13", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51933764", + "status": "PASS", + "utc": "20260916T111315Z" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fit_spec.json b/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..98ca678907eb621df281f83646e4b32f2373060a --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_EMP_CHB", + "g": 0, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CHB/r00000000/n32" + ], + "rep": 0, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..556f805651dbfae2c6218f1838a947e152d19825 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +27157 7642 4587 3522 2768 2381 2446 2283 2043 1845 1711 1630 1754 1613 1548 1380 1419 1367 1369 1176 1278 1169 1147 1112 978 1096 1059 1050 1031 976 922 868 900 793 880 804 796 746 724 696 756 692 694 578 615 576 594 580 635 583 568 515 476 491 593 548 473 444 411 416 435 493 435 \ No newline at end of file diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..9f0a99fab3b11047f64baea46d8fe1545f6763d5 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g0/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g0/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 2 -randSeed 0 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..51d4a3fdff2f1b1d9fcf76210917156cdff6556f --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 14,528 changeTypes: 0 +maxLogL = -4151.692565020334 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 12,818 changeTypes: 1 +standardTime: 1.9989999894192987 generations: 51247.13 N: 33,848 changeTypes: 0 +maxLogL = -3237.145975061668 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 86,160 changeTypes: 2 +standardTime: 0.2704941774041894 generations: 2721.97 N: 1,150 changeTypes: 1 +standardTime: 0.28369072495436226 generations: 2752.32 N: 19,058 changeTypes: 0 +maxLogL = -367.38583216693723 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 101,725 changeTypes: 2 +standardTime: 0.0489687960875355 generations: 1600.69 N: 5,221 changeTypes: 1 +standardTime: 0.6762311942681881 generations: 8151.10 N: 262,386 changeTypes: 2 +standardTime: 1.0546224049152744 generations: 41448.75 N: 14,297 changeTypes: 0 +maxLogL = -351.24324872260513 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 86,160 changeTypes: 2 +standardTime: 0.2704941774041894 generations: 2721.97 N: 1,150 changeTypes: 1 +standardTime: 0.28369072495436226 generations: 2752.32 N: 19,058 changeTypes: 0 +maxLogL = -367.38583216693723 + +computing time = 693.11 seconds diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fitcoal/output.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..3ee1967886dee87d5c5229099edc285327446f1e --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fitcoal/output.txt @@ -0,0 +1,106 @@ +year popSize +2000 3614 +2007 3573 +2014 3532 +2022 3492 +2029 3452 +2036 3413 +2043 3374 +2051 3335 +2058 3297 +2065 3260 +2072 3223 +2079 3186 +2087 3150 +2094 3114 +2101 3078 +2108 3043 +2116 3009 +2123 2975 +2130 2941 +2137 2907 +2144 2874 +2152 2841 +2159 2809 +2166 2777 +2173 2745 +2180 2714 +2188 2683 +2195 2653 +2202 2623 +2209 2593 +2217 2563 +2224 2534 +2231 2505 +2238 2477 +2245 2448 +2253 2421 +2260 2393 +2267 2366 +2274 2339 +2282 2312 +2289 2286 +2296 2260 +2303 2234 +2310 2209 +2318 2184 +2325 2159 +2332 2134 +2339 2110 +2347 2086 +2354 2062 +2361 2039 +2368 2015 +2375 1993 +2383 1970 +2390 1947 +2397 1925 +2404 1903 +2412 1882 +2419 1860 +2426 1839 +2433 1818 +2440 1797 +2448 1777 +2455 1757 +2462 1737 +2469 1717 +2476 1697 +2484 1678 +2491 1659 +2498 1640 +2505 1621 +2513 1603 +2520 1585 +2527 1567 +2534 1549 +2541 1531 +2549 1514 +2556 1497 +2563 1480 +2570 1463 +2578 1446 +2585 1430 +2592 1413 +2599 1397 +2606 1381 +2614 1366 +2621 1350 +2628 1335 +2635 1319 +2643 1304 +2650 1290 +2657 1275 +2664 1260 +2671 1246 +2679 1232 +2686 1218 +2693 1204 +2700 1190 +2708 1177 +2715 1163 +2722 1150 +2752 1150 +2752 19058 +4000000 19058 + diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..a58943a48f97b8f2d3333cf34f4a28b685cf1127 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 2 (recommended) +The proportion of truncated or collapsed SFS types: 0.031746031746031744 + diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/receipt_51933764.json b/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/receipt_51933764.json new file mode 100644 index 0000000000000000000000000000000000000000..df10008369d0a851a70c4bab152fb38bc51a580d --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/receipt_51933764.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "2a40c2b1c02b847c96294a30608bee77899b609be84525d7979b21a6aa3c7f36", + "elapsed_s": 704, + "failure_sha256": null, + "host": "cn604-13", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51933764", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "97093c99053f2979be18406d4eb20df6d6e2657862174fb8b91de2607daeb1c6", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:24:57Z" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/submissions.jsonl b/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..a58b57ca6b84cfd7eb76be4434927f5116253016 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g0/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g0/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CHB/receipts/export_51933097.json"], "job_id": "51933764", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_EMP_CHB/fitcoal_g0.json", "request_sha256": "379d48d5e1c145b2da793af7d8571c6e9fd096e0548b503b60c15bb6e5119795", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [0], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "97093c99053f2979be18406d4eb20df6d6e2657862174fb8b91de2607daeb1c6", "stage": "v2", "usage_before": {"account_jobs": 152, "bench_cores": 434, "bench_gpus": 20, "bench_jobs": 81, "bench_pending": 18, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:13:10Z"} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/envlock_check_51933766.json b/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/envlock_check_51933766.json new file mode 100644 index 0000000000000000000000000000000000000000..466943813c520cca7c97094a083da6163c47ffd2 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/envlock_check_51933766.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-10", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51933766", + "status": "PASS", + "utc": "20260916T111339Z" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fit_spec.json b/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..d0e539e2cfc26bbd8aa5d5d2c0897a811bfd52d3 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_EMP_CHB", + "g": 1, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CHB/r00000001/n32" + ], + "rep": 1, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..f79133ae9a908902e0ba8358a2323bd85c4235c3 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +26397 7710 4900 3648 2789 2522 2131 2250 1947 1921 1929 1843 1627 1665 1537 1510 1415 1231 1225 1210 1241 1134 1099 1039 979 1020 1024 945 999 937 908 809 785 790 853 807 815 744 667 786 670 667 720 653 708 579 602 648 633 608 559 641 554 521 513 460 445 428 444 517 485 471 341 \ No newline at end of file diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..04a357192e862a3f999f8dc8a17900a0aa62c5dd --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g1/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g1/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 4 -randSeed 1 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..18979c685a082df02b93076dcdefcb86c02e520b --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 14,417 changeTypes: 0 +maxLogL = -3688.776496915182 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 12,686 changeTypes: 1 +standardTime: 1.998999977128388 generations: 50719.26 N: 34,519 changeTypes: 0 +maxLogL = -2750.9484968332126 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 77,201 changeTypes: 2 +standardTime: 0.06439650427822106 generations: 1783.29 N: 4,624 changeTypes: 1 +standardTime: 0.3431085842623161 generations: 4360.71 N: 19,217 changeTypes: 0 +maxLogL = -368.4980724611478 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 83,835 changeTypes: 2 +standardTime: 0.05277465266540536 generations: 1620.60 N: 5,172 changeTypes: 2 +standardTime: 0.7687143627536038 generations: 17513.80 N: 30,872 changeTypes: 1 +standardTime: 1.9019736026882172 generations: 87484.84 N: 1,478 changeTypes: 0 +maxLogL = -365.5118486731312 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 77,201 changeTypes: 2 +standardTime: 0.06439650427822106 generations: 1783.29 N: 4,624 changeTypes: 1 +standardTime: 0.3431085842623161 generations: 4360.71 N: 19,217 changeTypes: 0 +maxLogL = -368.4980724611478 + +computing time = 833.42 seconds diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fitcoal/output.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..5fb3f142d77ae00e0d7c902f6e21faa75823e0c6 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 4624 +4361 4624 +4361 19217 +4000000 19217 + diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..f17274d89d9d62d06ab72eba6a878b5eb095d46b --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 4 (recommended) +The proportion of truncated or collapsed SFS types: 0.06349206349206349 + diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/receipt_51933766.json b/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/receipt_51933766.json new file mode 100644 index 0000000000000000000000000000000000000000..aea13bc12d45f6e47f4314ea2129bd955f1c58e5 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/receipt_51933766.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "c4ddadd180d6049d07f7bc8c416851f01504c5430451b1fa8a23b57771e3db87", + "elapsed_s": 860, + "failure_sha256": null, + "host": "cn604-10", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51933766", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "6b0c9ea67353f8e9f96d15508864b94ebd4288d00041638476302c4410ce0e43", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:27:42Z" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/submissions.jsonl b/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..233daf10c169e583acd823bb9d55cff85fe57d8e --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g1/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g1/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CHB/receipts/export_51933097.json"], "job_id": "51933766", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_EMP_CHB/fitcoal_g1.json", "request_sha256": "9b91cf08d4f0895784cead3187429b4e30f0e8c506f962b56fac0c8bbdbc7269", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [1], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "6b0c9ea67353f8e9f96d15508864b94ebd4288d00041638476302c4410ce0e43", "stage": "v2", "usage_before": {"account_jobs": 152, "bench_cores": 434, "bench_gpus": 20, "bench_jobs": 81, "bench_pending": 18, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:13:18Z"} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/envlock_check_51933767.json b/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/envlock_check_51933767.json new file mode 100644 index 0000000000000000000000000000000000000000..e105a6c6d504ec4846b1d88f1bd4b1572a29fbe4 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/envlock_check_51933767.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-10", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51933767", + "status": "PASS", + "utc": "20260916T111330Z" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fit_spec.json b/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..769736524dd5307c60ffb0270686e96ebd0d9f4e --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_EMP_CHB", + "g": 2, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CHB/r00000002/n32" + ], + "rep": 2, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..cb4f0559923a76441690ff18a848dbf1789ddf04 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +27127 7782 4748 3498 2982 2707 2347 2060 2026 1837 1788 1662 1525 1573 1408 1470 1280 1164 1222 1231 1176 1097 1061 1029 1009 1015 913 1038 949 905 845 745 866 842 801 888 717 757 726 692 691 613 646 623 583 542 575 590 626 566 468 515 539 518 498 486 493 450 522 385 497 470 491 \ No newline at end of file diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..1d267353dd0c3ad69479a164e04c131bff3a801c --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g2/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g2/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 5 -randSeed 2 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..e7cb2e06c2fcf12b1664b53144a833792c9a331f --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 14,281 changeTypes: 0 +maxLogL = -3537.730217029351 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 157,082 changeTypes: 1 +standardTime: 0.0010501911807336644 generations: 329.93 N: 13,258 changeTypes: 0 +maxLogL = -2651.050735728533 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 107,117 changeTypes: 2 +standardTime: 0.03877198719760506 generations: 1437.71 N: 6,102 changeTypes: 1 +standardTime: 0.39071807772191564 generations: 5732.94 N: 18,751 changeTypes: 0 +maxLogL = -322.95907895611754 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 121,583 changeTypes: 2 +standardTime: 0.031123416443463878 generations: 1295.87 N: 6,822 changeTypes: 1 +standardTime: 0.7260192545364718 generations: 10776.89 N: 54,794 changeTypes: 1 +standardTime: 1.000975739825937 generations: 40908.72 N: 13,149 changeTypes: 0 +maxLogL = -317.8102225060975 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 107,117 changeTypes: 2 +standardTime: 0.03877198719760506 generations: 1437.71 N: 6,102 changeTypes: 1 +standardTime: 0.39071807772191564 generations: 5732.94 N: 18,751 changeTypes: 0 +maxLogL = -322.95907895611754 + +computing time = 817.00 seconds diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fitcoal/output.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..3299c6c1a5533644be22041075aa269f4f4415a4 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 6102 +5733 6102 +5733 18751 +4000000 18751 + diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..90ca5e6d1453dbb07f128679466e8385cc5821b9 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 5 (recommended) +The proportion of truncated or collapsed SFS types: 0.07936507936507936 + diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/receipt_51933767.json b/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/receipt_51933767.json new file mode 100644 index 0000000000000000000000000000000000000000..7ac27e21996726e159773b48249be4e83dac1c74 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/receipt_51933767.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "def9d69eb45f2e8f9c33c8bf49d049b5d2182aed21cf7742ecb181dc7850e475", + "elapsed_s": 835, + "failure_sha256": null, + "host": "cn604-10", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51933767", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "f3a89fb8f4069793a531347a7a94ca2ab4e3220106f65c1cb7c4a86a66dacd20", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:27:20Z" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/submissions.jsonl b/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..72471cb6bf6fbb31a8f81fa4b42bec6d5f438d5e --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g2/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g2/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CHB/receipts/export_51933097.json"], "job_id": "51933767", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_EMP_CHB/fitcoal_g2.json", "request_sha256": "162ff724738ca0ae51f9fcc04bd3800ef71c06bfbda27b19c9960b35d60d4230", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [2], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "f3a89fb8f4069793a531347a7a94ca2ab4e3220106f65c1cb7c4a86a66dacd20", "stage": "v2", "usage_before": {"account_jobs": 153, "bench_cores": 436, "bench_gpus": 20, "bench_jobs": 82, "bench_pending": 17, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:13:23Z"} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/envlock_check_51933768.json b/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/envlock_check_51933768.json new file mode 100644 index 0000000000000000000000000000000000000000..630ab1fafcd0b23b1c10cbe8144cdb7f62d2dd0a --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/envlock_check_51933768.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-18", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51933768", + "status": "PASS", + "utc": "20260916T111333Z" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fit_spec.json b/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..8dbe5d91a2df20343656433301a355c8fe24ff5a --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_EMP_CHB", + "g": 3, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CHB/r00000003/n32" + ], + "rep": 3, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..23ac8efedae43f989153091e045e369a9b258d21 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +26583 7797 4789 3593 2988 2470 2257 2323 1902 1811 1775 1627 1629 1538 1511 1482 1318 1416 1153 1219 1138 1123 1033 949 1113 1044 989 1063 965 889 841 899 842 790 839 922 811 711 749 615 655 639 621 612 582 655 599 559 590 599 563 561 593 517 554 607 507 394 473 531 444 401 524 \ No newline at end of file diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..79a29f99a340f86684861ddda3bd5e4356ffa06b --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g3/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g3/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 6 -randSeed 3 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..fc9d80b6662d195b51597e9afdbf0ffe9e50ae06 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 14,333 changeTypes: 0 +maxLogL = -3639.6782368364325 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 12,661 changeTypes: 1 +standardTime: 1.9989999969638315 generations: 50620.49 N: 34,307 changeTypes: 0 +maxLogL = -2759.407131380636 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 89,212 changeTypes: 2 +standardTime: 0.04369065360281302 generations: 1505.97 N: 5,937 changeTypes: 1 +standardTime: 0.4150259734032926 generations: 5914.98 N: 19,556 changeTypes: 0 +maxLogL = -349.0809022925928 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 149,096 changeTypes: 1 +standardTime: 0.001483180822257521 generations: 442.27 N: 17,732 changeTypes: 2 +standardTime: 0.24384564536890008 generations: 3531.45 N: 2,969 changeTypes: 2 +standardTime: 0.3948761667192246 generations: 5519.42 N: 19,413 changeTypes: 0 +maxLogL = -346.9555763999192 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 89,212 changeTypes: 2 +standardTime: 0.04369065360281302 generations: 1505.97 N: 5,937 changeTypes: 1 +standardTime: 0.4150259734032926 generations: 5914.98 N: 19,556 changeTypes: 0 +maxLogL = -349.0809022925928 + +computing time = 728.37 seconds diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fitcoal/output.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..5c837a4d5acb457469a213e78b1afc14ae835474 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 5937 +5915 5937 +5915 19556 +4000000 19556 + diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..840145fee15c1f0c97f65692dd0d6359c6fcd788 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 6 (recommended) +The proportion of truncated or collapsed SFS types: 0.09523809523809523 + diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/receipt_51933768.json b/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/receipt_51933768.json new file mode 100644 index 0000000000000000000000000000000000000000..ee7761e2ad0193e20602bba2c98294bebc016b5a --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/receipt_51933768.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "52854770f8932ca6a8b1968e0da66bf1c3fdddec084cee4aedfed7c15381d510", + "elapsed_s": 739, + "failure_sha256": null, + "host": "cn604-18", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51933768", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "3977268394790f6a7784ccbf6c647360cfc0708b0e443cd5048ae22eecf8b127", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:25:51Z" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/submissions.jsonl b/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..02ea401070632cf25a1174741deea4e30529df6b --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g3/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g3/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CHB/receipts/export_51933097.json"], "job_id": "51933768", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_EMP_CHB/fitcoal_g3.json", "request_sha256": "c3da1cce0ea9acf4d298279a55016f7cf63a4519c1dc1b307d8c8bf7ecae8609", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [3], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "3977268394790f6a7784ccbf6c647360cfc0708b0e443cd5048ae22eecf8b127", "stage": "v2", "usage_before": {"account_jobs": 154, "bench_cores": 438, "bench_gpus": 20, "bench_jobs": 83, "bench_pending": 17, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:13:27Z"} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/envlock_check_51933769.json b/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/envlock_check_51933769.json new file mode 100644 index 0000000000000000000000000000000000000000..476b735bf3dab2f3391692faf12e3a858e4773e9 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/envlock_check_51933769.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-18", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51933769", + "status": "PASS", + "utc": "20260916T111417Z" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fit_spec.json b/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..5280052f97f879878223dfb177ef5b5838435ff8 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_EMP_CHB", + "g": 4, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CHB/r00000004/n32" + ], + "rep": 4, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..6324c857ad9f6aeeddbd378c379d155961bf7220 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +26480 7433 4537 3369 2871 2624 2359 2146 1994 1935 1893 1863 1789 1677 1712 1496 1365 1243 1162 1256 1197 1195 1111 1087 1178 1055 1067 915 879 919 996 830 979 859 806 840 764 797 758 668 633 588 632 611 575 605 614 581 646 589 569 518 523 518 469 507 512 487 451 434 410 453 541 \ No newline at end of file diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..1aac02b268e8ba3af5690979a470aefcba7634e6 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g4/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g4/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 1 -randSeed 4 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..593a9e6dbaa3cb836b2e0f26234f3206228d6c9c --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 14,434 changeTypes: 0 +maxLogL = -4010.929650463097 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 12,678 changeTypes: 1 +standardTime: 1.9989999451101352 generations: 50686.13 N: 34,017 changeTypes: 0 +maxLogL = -3041.7986288469615 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 94,281 changeTypes: 2 +standardTime: 0.24915128383538213 generations: 2472.75 N: 1,102 changeTypes: 1 +standardTime: 0.26050362771306035 generations: 2497.78 N: 18,752 changeTypes: 0 +maxLogL = -371.27856703029147 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 100,677 changeTypes: 2 +standardTime: 0.07464177588430164 generations: 1777.74 N: 3,395 changeTypes: 2 +standardTime: 0.43503673978075363 generations: 7181.71 N: 21,964 changeTypes: 1 +standardTime: 1.9989923790667234 generations: 75884.29 N: 11,513 changeTypes: 0 +maxLogL = -367.94149369474826 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 94,281 changeTypes: 2 +standardTime: 0.24915128383538213 generations: 2472.75 N: 1,102 changeTypes: 1 +standardTime: 0.26050362771306035 generations: 2497.78 N: 18,752 changeTypes: 0 +maxLogL = -371.27856703029147 + +computing time = 690.64 seconds diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fitcoal/output.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..04066da3b27c6ba00787cdb5d2459bffea2fb6a3 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fitcoal/output.txt @@ -0,0 +1,106 @@ +year popSize +2000 2581 +2005 2559 +2009 2537 +2014 2516 +2019 2494 +2024 2473 +2028 2452 +2033 2431 +2038 2411 +2043 2390 +2047 2370 +2052 2350 +2057 2330 +2061 2310 +2066 2291 +2071 2272 +2076 2252 +2080 2233 +2085 2214 +2090 2196 +2095 2177 +2099 2158 +2104 2140 +2109 2122 +2113 2104 +2118 2086 +2123 2069 +2128 2051 +2132 2034 +2137 2017 +2142 1999 +2147 1982 +2151 1966 +2156 1949 +2161 1933 +2165 1916 +2170 1900 +2175 1884 +2180 1868 +2184 1852 +2189 1836 +2194 1821 +2199 1805 +2203 1790 +2208 1775 +2213 1760 +2217 1745 +2222 1730 +2227 1716 +2232 1701 +2236 1687 +2241 1672 +2246 1658 +2251 1644 +2255 1630 +2260 1616 +2265 1603 +2269 1589 +2274 1576 +2279 1562 +2284 1549 +2288 1536 +2293 1523 +2298 1510 +2303 1497 +2307 1485 +2312 1472 +2317 1460 +2321 1447 +2326 1435 +2331 1423 +2336 1411 +2340 1399 +2345 1387 +2350 1375 +2355 1364 +2359 1352 +2364 1341 +2369 1329 +2373 1318 +2378 1307 +2383 1296 +2388 1285 +2392 1274 +2397 1263 +2402 1252 +2407 1242 +2411 1231 +2416 1221 +2421 1211 +2425 1200 +2430 1190 +2435 1180 +2440 1170 +2444 1160 +2449 1150 +2454 1141 +2459 1131 +2463 1121 +2468 1112 +2473 1102 +2498 1102 +2498 18752 +4000000 18752 + diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..5dc872fd79c57a0630616d4dc65b24263eb0d126 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 1 (recommended) +The proportion of truncated or collapsed SFS types: 0.015873015873015872 + diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/receipt_51933769.json b/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/receipt_51933769.json new file mode 100644 index 0000000000000000000000000000000000000000..5694772e33bc9e9e1d40ab5f03c90a1259f16462 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/receipt_51933769.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "f6ebae8a434b532f9226439b313a439789a51270ff6ef185db5b40f61d5ac07c", + "elapsed_s": 727, + "failure_sha256": null, + "host": "cn604-18", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51933769", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "de702c0a3bfb0002ba2bbef00a416d4813b810a376e333c9bb8fd7a2c6a7a272", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:25:58Z" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/submissions.jsonl b/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..8b453ae990f2d900fb37beccdc457cdc089d2452 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g4/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g4/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CHB/receipts/export_51933097.json"], "job_id": "51933769", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_EMP_CHB/fitcoal_g4.json", "request_sha256": "74bb4f9cfdf0f377e141006d738a9012af9c4a5e1b7af325fd2c4b1ff9c112eb", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [4], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "de702c0a3bfb0002ba2bbef00a416d4813b810a376e333c9bb8fd7a2c6a7a272", "stage": "v2", "usage_before": {"account_jobs": 150, "bench_cores": 425, "bench_gpus": 20, "bench_jobs": 79, "bench_pending": 17, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:13:49Z"} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/envlock_check_51933770.json b/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/envlock_check_51933770.json new file mode 100644 index 0000000000000000000000000000000000000000..cf4c3045f2b1ef52219cb7cba90eb1e42cc2139c --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/envlock_check_51933770.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-07", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51933770", + "status": "PASS", + "utc": "20260916T111625Z" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fit_spec.json b/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..17957364cf534a8753957f0c0ecf56a7efaba49e --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_EMP_CHB", + "g": 5, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CHB/r00000005/n32" + ], + "rep": 5, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..f547b6d62cb9a91307810c6f57171ce3626beaa6 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +27039 7809 4392 3590 2909 2725 2519 2261 2073 1987 1788 1646 1663 1319 1485 1348 1259 1217 1218 1104 1133 1023 1102 1094 987 923 983 896 865 932 864 759 858 760 767 745 728 686 639 771 709 621 629 618 620 582 584 553 553 552 547 540 520 615 530 536 519 563 466 466 468 500 511 \ No newline at end of file diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..9015743cc2c19da48c05aa93312601bebae2ce14 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g5/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g5/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 1 -randSeed 5 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..6a5a855ccd66cbcc5dd1c2aad4d359d1714cc7c6 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 14,311 changeTypes: 0 +maxLogL = -3611.3993540725132 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 1,067,047 changeTypes: 2 +standardTime: 0.0038314274324794 generations: 453.10 N: 13,321 changeTypes: 0 +maxLogL = -2773.444734845788 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 56,831 changeTypes: 1 +standardTime: 0.008592007196827052 generations: 976.59 N: 5,963 changeTypes: 2 +standardTime: 0.6337933360291813 generations: 13629.07 N: 19,223 changeTypes: 0 +maxLogL = -351.55394798861107 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 46,824 changeTypes: 1 +standardTime: 0.013948210830050082 generations: 1306.21 N: 936 changeTypes: 1 +standardTime: 0.07830103487243197 generations: 1426.67 N: 9,944 changeTypes: 1 +standardTime: 0.6509497670803085 generations: 12815.90 N: 19,806 changeTypes: 0 +maxLogL = -340.40277039668536 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 56,831 changeTypes: 1 +standardTime: 0.008592007196827052 generations: 976.59 N: 5,963 changeTypes: 2 +standardTime: 0.6337933360291813 generations: 13629.07 N: 19,223 changeTypes: 0 +maxLogL = -351.55394798861107 + +computing time = 676.84 seconds diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fitcoal/output.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..9a70bf1c1dffa383f76896f0be491be23aa57277 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fitcoal/output.txt @@ -0,0 +1,104 @@ +year popSize +2000 6555 +2116 6626 +2233 6698 +2349 6770 +2465 6843 +2581 6917 +2698 6992 +2814 7068 +2930 7144 +3047 7222 +3163 7300 +3279 7379 +3395 7459 +3512 7539 +3628 7621 +3744 7703 +3861 7787 +3977 7871 +4093 7956 +4210 8042 +4326 8129 +4442 8217 +4558 8306 +4675 8396 +4791 8486 +4907 8578 +5024 8671 +5140 8765 +5256 8860 +5372 8955 +5489 9052 +5605 9150 +5721 9249 +5838 9349 +5954 9450 +6070 9552 +6186 9656 +6303 9760 +6419 9866 +6535 9973 +6652 10080 +6768 10189 +6884 10300 +7000 10411 +7117 10524 +7233 10637 +7349 10753 +7466 10869 +7582 10986 +7698 11105 +7815 11225 +7931 11347 +8047 11470 +8163 11594 +8280 11719 +8396 11846 +8512 11974 +8629 12103 +8745 12234 +8861 12367 +8977 12500 +9094 12636 +9210 12772 +9326 12910 +9443 13050 +9559 13191 +9675 13334 +9791 13478 +9908 13624 +10024 13771 +10140 13920 +10257 14071 +10373 14223 +10489 14377 +10606 14532 +10722 14690 +10838 14848 +10954 15009 +11071 15171 +11187 15335 +11303 15501 +11420 15669 +11536 15839 +11652 16010 +11768 16183 +11885 16358 +12001 16535 +12117 16714 +12234 16895 +12350 17077 +12466 17262 +12582 17449 +12699 17638 +12815 17828 +12931 18021 +13048 18216 +13164 18413 +13280 18612 +13396 18814 +13513 19017 +13629 19223 +4000000 19223 + diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..5dc872fd79c57a0630616d4dc65b24263eb0d126 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 1 (recommended) +The proportion of truncated or collapsed SFS types: 0.015873015873015872 + diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/receipt_51933770.json b/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/receipt_51933770.json new file mode 100644 index 0000000000000000000000000000000000000000..971c286ec4f745998fffa4801287051bbb401c3c --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/receipt_51933770.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "e1d6d5fe5d085b0c259fb2fb0fa348e79965be4476b9e7320dfc39bf13fd38e1", + "elapsed_s": 840, + "failure_sha256": null, + "host": "cn604-07", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51933770", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "37a89a85748c934c474f8cd85aa604623bbc3a9346ad80a64153aed5184ac545", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:27:53Z" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/submissions.jsonl b/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..9b1d0f8016cb19eb3898a14542d086af7e524a05 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g5/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g5/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CHB/receipts/export_51933097.json"], "job_id": "51933770", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_EMP_CHB/fitcoal_g5.json", "request_sha256": "dd6c83e70db0661a5aefbe868ce3b50b735ebc4a7a8f4b1a26b7df36f119dc1f", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [5], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "37a89a85748c934c474f8cd85aa604623bbc3a9346ad80a64153aed5184ac545", "stage": "v2", "usage_before": {"account_jobs": 151, "bench_cores": 427, "bench_gpus": 20, "bench_jobs": 80, "bench_pending": 18, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:13:51Z"} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/envlock_check_51933804.json b/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/envlock_check_51933804.json new file mode 100644 index 0000000000000000000000000000000000000000..9bae83af3af209cd31603b05aac831dca5116142 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/envlock_check_51933804.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn511-13", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51933804", + "status": "PASS", + "utc": "20260916T111402Z" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fit_spec.json b/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..dd7da55c1dc7fa28537f967e018c60f82014f2f1 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_EMP_CHB", + "g": 6, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CHB/r00000006/n32" + ], + "rep": 6, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..d6635308bdf58c34a39e82c0b20932f5115b2790 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +27159 7634 4677 3537 2970 2264 2102 2088 1887 1787 1810 1620 1559 1469 1331 1366 1294 1299 1240 1146 1181 1036 1030 1079 994 939 1069 877 923 856 866 731 888 779 749 667 786 686 702 733 671 590 705 675 602 657 599 618 550 554 516 554 561 526 443 500 553 452 571 512 541 484 427 \ No newline at end of file diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..7ab8ca86767cb331c25b20fbe5076293a5dbd39d --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g6/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g6/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 6 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..d6903686569de36c7080ef16b6ca29a2e9b3cd53 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 14,194 changeTypes: 0 +maxLogL = -4033.1324778738053 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 829,901 changeTypes: 2 +standardTime: 0.004182490553294128 generations: 463.53 N: 13,159 changeTypes: 0 +maxLogL = -3102.5259112988347 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 104,064 changeTypes: 2 +standardTime: 0.04049030489569249 generations: 1480.08 N: 6,051 changeTypes: 1 +standardTime: 0.4553649497817618 generations: 6501.09 N: 19,307 changeTypes: 0 +maxLogL = -378.97705249367436 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 453,730 changeTypes: 2 +standardTime: 0.008549545899236472 generations: 742.85 N: 11,528 changeTypes: 1 +standardTime: 0.07499499937926533 generations: 2274.87 N: 2,840 changeTypes: 2 +standardTime: 0.45605325737509417 generations: 7121.69 N: 19,111 changeTypes: 0 +maxLogL = -373.93383958213326 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 104,064 changeTypes: 2 +standardTime: 0.04049030489569249 generations: 1480.08 N: 6,051 changeTypes: 1 +standardTime: 0.4553649497817618 generations: 6501.09 N: 19,307 changeTypes: 0 +maxLogL = -378.97705249367436 + +computing time = 632.20 seconds diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fitcoal/output.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..47ac27e33f29e209adb68b4d94ee426cec96091d --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 6051 +6501 6051 +6501 19307 +4000000 19307 + diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/receipt_51933804.json b/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/receipt_51933804.json new file mode 100644 index 0000000000000000000000000000000000000000..904cc0c633710d06d37274736afb0f43953aac10 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/receipt_51933804.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "501a0b35a6e29cd9065cb270615ca6cea85883756975e9fa96e07864f9696f0b", + "elapsed_s": 651, + "failure_sha256": null, + "host": "cn511-13", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51933804", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "ae99d9c6b35f34a08bfc504160a218fc6b5e48c5dc21fba1ea0528040512a5be", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:24:50Z" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/submissions.jsonl b/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..0763cb4c050d6a1bb3a8de737f23891a50b6c0dc --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g6/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g6/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CHB/receipts/export_51933097.json"], "job_id": "51933804", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_EMP_CHB/fitcoal_g6.json", "request_sha256": "1a44ada25b6268dd75429f2fa38c5ae06df8671dbc7cc9b63215d3f49d031321", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [6], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "ae99d9c6b35f34a08bfc504160a218fc6b5e48c5dc21fba1ea0528040512a5be", "stage": "v2", "usage_before": {"account_jobs": 152, "bench_cores": 429, "bench_gpus": 20, "bench_jobs": 81, "bench_pending": 17, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:13:55Z"} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/envlock_check_51933809.json b/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/envlock_check_51933809.json new file mode 100644 index 0000000000000000000000000000000000000000..ba773d4c456f6a71971c01c4dad09aeb85bec1b0 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/envlock_check_51933809.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-07", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51933809", + "status": "PASS", + "utc": "20260916T111410Z" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fit_spec.json b/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..9b577b28d8b06cdeda42f9b0f5cb1278b8ce060b --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_EMP_CHB", + "g": 7, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CHB/r00000007/n32" + ], + "rep": 7, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..baf7b54232cb970eab702440baf608d4d2428584 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +26619 7842 4806 3311 2916 2628 2188 2032 1878 1856 1759 1682 1640 1438 1456 1433 1329 1435 1260 1285 1211 1146 1087 1055 1084 972 1010 927 1012 926 853 898 747 847 784 785 825 764 681 649 638 586 629 630 635 562 566 537 580 539 510 509 555 572 478 506 424 519 438 370 430 390 514 \ No newline at end of file diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..816a5ac6df48fd8759c3072465095a564d62165d --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g7/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g7/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 1 -randSeed 7 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..1201fc0bc8b37f72f0339f55647216bf2005b671 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 14,240 changeTypes: 0 +maxLogL = -3677.4931735447217 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 526,546 changeTypes: 2 +standardTime: 0.004100798715385242 generations: 411.94 N: 13,312 changeTypes: 0 +maxLogL = -2930.1246397263767 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 69,283 changeTypes: 2 +standardTime: 0.27265153912188494 generations: 2898.67 N: 1,316 changeTypes: 1 +standardTime: 0.28577119949492985 generations: 2933.19 N: 18,339 changeTypes: 0 +maxLogL = -358.92225804689065 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 73,838 changeTypes: 2 +standardTime: 0.06563300263395629 generations: 1850.18 N: 4,831 changeTypes: 1 +standardTime: 0.6056456293450452 generations: 7067.47 N: 419,070 changeTypes: 2 +standardTime: 0.7907965296277212 generations: 27155.76 N: 15,971 changeTypes: 0 +maxLogL = -348.3416320812755 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 69,283 changeTypes: 2 +standardTime: 0.27265153912188494 generations: 2898.67 N: 1,316 changeTypes: 1 +standardTime: 0.28577119949492985 generations: 2933.19 N: 18,339 changeTypes: 0 +maxLogL = -358.92225804689065 + +computing time = 649.46 seconds diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fitcoal/output.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..6af65e205cf15f071645b4568f3a0c7927f4a902 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fitcoal/output.txt @@ -0,0 +1,106 @@ +year popSize +2000 4496 +2009 4441 +2018 4387 +2027 4333 +2036 4280 +2045 4228 +2054 4176 +2063 4125 +2072 4075 +2081 4025 +2090 3976 +2099 3928 +2108 3880 +2117 3832 +2126 3785 +2135 3739 +2144 3693 +2153 3648 +2162 3604 +2171 3560 +2180 3516 +2189 3473 +2198 3431 +2207 3389 +2216 3348 +2225 3307 +2234 3266 +2243 3226 +2252 3187 +2261 3148 +2270 3110 +2279 3072 +2288 3034 +2297 2997 +2306 2960 +2315 2924 +2324 2889 +2333 2853 +2341 2818 +2350 2784 +2359 2750 +2368 2716 +2377 2683 +2386 2650 +2395 2618 +2404 2586 +2413 2555 +2422 2523 +2431 2493 +2440 2462 +2449 2432 +2458 2402 +2467 2373 +2476 2344 +2485 2315 +2494 2287 +2503 2259 +2512 2232 +2521 2204 +2530 2177 +2539 2151 +2548 2125 +2557 2099 +2566 2073 +2575 2048 +2584 2023 +2593 1998 +2602 1973 +2611 1949 +2620 1926 +2629 1902 +2638 1879 +2647 1856 +2656 1833 +2665 1811 +2674 1789 +2683 1767 +2692 1745 +2701 1724 +2710 1703 +2719 1682 +2728 1662 +2737 1641 +2746 1621 +2755 1601 +2764 1582 +2773 1563 +2782 1543 +2791 1525 +2800 1506 +2809 1488 +2818 1469 +2827 1451 +2836 1434 +2845 1416 +2854 1399 +2863 1382 +2872 1365 +2881 1348 +2890 1332 +2899 1316 +2933 1316 +2933 18339 +4000000 18339 + diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..5dc872fd79c57a0630616d4dc65b24263eb0d126 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 1 (recommended) +The proportion of truncated or collapsed SFS types: 0.015873015873015872 + diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/receipt_51933809.json b/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/receipt_51933809.json new file mode 100644 index 0000000000000000000000000000000000000000..2a533a78dd9a88d0aeba6ca085ed1d255f60e436 --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/receipt_51933809.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "3186c090ebd49b24aebc2ef1dc7b22f7805acb8db51bfd7f962c740ae7e6c71c", + "elapsed_s": 675, + "failure_sha256": null, + "host": "cn604-07", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51933809", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "c4523d8d50c580dc6c53e5232f11e27504f162a5115194aa872b8378cdaf59c0", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:25:17Z" +} diff --git a/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/submissions.jsonl b/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..bf82cb62b5e4b215d5a5d1e5f69eb1bcbe295e4b --- /dev/null +++ b/estimates/fitcoal/a1/EMP_CHB/K1/g7/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_EMP_CHB/K1/g7/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_EMP_CHB/receipts/export_51933097.json"], "job_id": "51933809", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_EMP_CHB/fitcoal_g7.json", "request_sha256": "310cffab2c61691f3d8f06d2ee07173adcc741cee04e1cd631d1ceed92febc7d", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [7], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "c4523d8d50c580dc6c53e5232f11e27504f162a5115194aa872b8378cdaf59c0", "stage": "v2", "usage_before": {"account_jobs": 153, "bench_cores": 431, "bench_gpus": 20, "bench_jobs": 82, "bench_pending": 17, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:13:59Z"} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/envlock_check_51934453.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/envlock_check_51934453.json new file mode 100644 index 0000000000000000000000000000000000000000..4f70b800458ed01c61f79969c28906c37d622856 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/envlock_check_51934453.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-14", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51934453", + "status": "PASS", + "utc": "20260916T112101Z" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fit_spec.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..80f8f817ec0116fed027fd106e512f686f7d68ea --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_GROW_X100_300", + "g": 0, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_GROW_X100_300/r00000000/n32" + ], + "rep": 0, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..a6355b7af3334ef313219443a1b5b93a79a96960 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +20903 7786 5128 3964 2993 2531 2309 1942 1663 1650 1360 1216 1098 1118 1009 938 883 838 760 738 692 712 684 687 644 606 627 503 517 538 478 510 502 446 531 436 418 401 337 369 357 337 352 371 320 347 332 249 288 237 232 268 257 299 249 280 241 227 235 273 204 246 194 \ No newline at end of file diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..51552201c0826101d76399273f5b1396a7527ca2 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g0/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g0/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 0 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..af696cbd374c25fe7720b1a2a5efdbb8b1a0c3de --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 10,978 changeTypes: 0 +maxLogL = -1071.8312704078821 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 175,390 changeTypes: 2 +standardTime: 0.006258496207439085 generations: 384.25 N: 10,150 changeTypes: 0 +maxLogL = -355.6841811080493 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 112,824 changeTypes: 1 +standardTime: 0.0011256854659876686 generations: 254.01 N: 10,383 changeTypes: 1 +standardTime: 1.7807989782967204 generations: 37210.36 N: 8,727 changeTypes: 0 +maxLogL = -344.9003940415013 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 175,390 changeTypes: 2 +standardTime: 0.006258496207439085 generations: 384.25 N: 10,150 changeTypes: 0 +maxLogL = -355.6841811080493 + +computing time = 129.90 seconds diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fitcoal/output.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..c5ff6f7cfaf7beb5c4acb6b9a20f76b80485b261 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 10150 +4000000 10150 + diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/receipt_51934453.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/receipt_51934453.json new file mode 100644 index 0000000000000000000000000000000000000000..506c964b9a4291c01f9aeff1ce763caec0550ddc --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/receipt_51934453.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "3c5735daaccf2935d671a64395058f3a0f6271e25c963544ea4a6f7e569531b8", + "elapsed_s": 143, + "failure_sha256": null, + "host": "cn604-14", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51934453", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "85d0ededd5b89eda01a066869fe6d9f1395baac721213522d53347adbbf60d49", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:23:21Z" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/submissions.jsonl b/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..7e74fea38cb4bdc89f683b9b3de260bd56ac853a --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g0/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g0/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_GROW_X100_300/receipts/export_51933106.json"], "job_id": "51934453", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_GROW_X100_300/fitcoal_g0.json", "request_sha256": "f8fe25a62f3b6120aa631c0301e9748203ad10da1e925a018c7382172b73d5f7", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [0], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "85d0ededd5b89eda01a066869fe6d9f1395baac721213522d53347adbbf60d49", "stage": "v2", "usage_before": {"account_jobs": 168, "bench_cores": 468, "bench_gpus": 17, "bench_jobs": 97, "bench_pending": 16, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:20:54Z"} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/envlock_check_51934454.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/envlock_check_51934454.json new file mode 100644 index 0000000000000000000000000000000000000000..5c1b172643c06d99768fb884c351e42a5817d858 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/envlock_check_51934454.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-12", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51934454", + "status": "PASS", + "utc": "20260916T112109Z" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fit_spec.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..19bc996a007a0513b7cf01ad1edc7ce27bd74dd8 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_GROW_X100_300", + "g": 1, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_GROW_X100_300/r00000001/n32" + ], + "rep": 1, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..4223d5ec83f0e0799a2dfb6a6978fd42ba2d8d9f --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +20334 7792 5239 3905 3006 2603 1974 1837 1675 1486 1386 1242 1161 1039 932 912 931 795 808 714 690 611 621 624 639 575 549 529 518 484 447 428 434 452 433 407 427 367 404 362 345 303 318 320 355 275 376 318 263 273 267 304 290 300 302 281 210 249 294 257 240 242 209 \ No newline at end of file diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..f3953681c8c46de6b2f7831e14ad0747f4004901 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g1/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g1/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 1 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..d64b1c7aed6412848a7ad94130eb206ae1cfb1e2 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 10,767 changeTypes: 0 +maxLogL = -989.0190316283122 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 45,998 changeTypes: 2 +standardTime: 0.014518432598828025 generations: 563.54 N: 9,925 changeTypes: 0 +maxLogL = -331.4049281829032 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 116,083 changeTypes: 2 +standardTime: 0.005803368040330445 generations: 328.49 N: 10,813 changeTypes: 2 +standardTime: 0.24557124914257447 generations: 5260.11 N: 9,789 changeTypes: 0 +maxLogL = -323.81969377323367 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 45,998 changeTypes: 2 +standardTime: 0.014518432598828025 generations: 563.54 N: 9,925 changeTypes: 0 +maxLogL = -331.4049281829032 + +computing time = 150.29 seconds diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fitcoal/output.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..90e98930298dda868c5fb7fc4d972cefc9cd0e82 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 9925 +4000000 9925 + diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/receipt_51934454.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/receipt_51934454.json new file mode 100644 index 0000000000000000000000000000000000000000..eb4a4c13fc95984cd37ed4d7dbf460bffe56b917 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/receipt_51934454.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "c31c775492572bcc37c1a66670b31a8f016b50a59a360a18318f584b0e71c641", + "elapsed_s": 167, + "failure_sha256": null, + "host": "cn604-12", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51934454", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "1f859354a24a532fb551b8df02d3c89924b26db204e8bb184b70b6d056517eda", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:23:48Z" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/submissions.jsonl b/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..616e0a4fd44078e6d6b3e71993f3010e0dc88fe6 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g1/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g1/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_GROW_X100_300/receipts/export_51933106.json"], "job_id": "51934454", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_GROW_X100_300/fitcoal_g1.json", "request_sha256": "af98cd6e9117c7b5a69d7a79385beffb4752661bbd17dad181bc5f2f46064459", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [1], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "1f859354a24a532fb551b8df02d3c89924b26db204e8bb184b70b6d056517eda", "stage": "v2", "usage_before": {"account_jobs": 169, "bench_cores": 470, "bench_gpus": 17, "bench_jobs": 98, "bench_pending": 17, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:20:58Z"} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/envlock_check_51934466.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/envlock_check_51934466.json new file mode 100644 index 0000000000000000000000000000000000000000..2e7b4de5fdcfc578cd85c16a655743a7730ef166 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/envlock_check_51934466.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-09", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51934466", + "status": "PASS", + "utc": "20260916T112137Z" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fit_spec.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..05d1bd45922e5ae03ddcd1c12e0b2abad6119f90 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_GROW_X100_300", + "g": 2, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_GROW_X100_300/r00000002/n32" + ], + "rep": 2, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..e37ebc46036406b342e933f3a9d7ee363a29442d --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +20263 7269 4870 3904 3119 2441 2168 1842 1608 1481 1291 1167 1158 1053 1007 890 817 811 773 645 728 727 703 636 648 620 527 523 503 504 477 540 469 427 390 421 456 357 391 354 402 330 340 292 290 308 278 319 296 292 316 262 276 277 306 219 231 304 300 311 280 204 247 \ No newline at end of file diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..05c1d2f98e39d3a38952894805fb45c240932960 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g2/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g2/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 4 -randSeed 2 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..9dfdc7ff047e98a3392cc24fc4ef5ad236c2f5e9 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 10,667 changeTypes: 0 +maxLogL = -1006.8816750391182 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 124,064 changeTypes: 1 +standardTime: 0.0010214213330747976 generations: 253.44 N: 9,880 changeTypes: 0 +maxLogL = -327.20764397750224 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 70,126 changeTypes: 1 +standardTime: 0.002541195954687849 generations: 356.41 N: 6,371 changeTypes: 2 +standardTime: 0.028978904296487768 generations: 773.58 N: 9,932 changeTypes: 0 +maxLogL = -324.8801871217091 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 124,064 changeTypes: 1 +standardTime: 0.0010214213330747976 generations: 253.44 N: 9,880 changeTypes: 0 +maxLogL = -327.20764397750224 + +computing time = 136.06 seconds diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fitcoal/output.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..11c92cc229372673692c60458f891be2e4925e8f --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 9880 +4000000 9880 + diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..f17274d89d9d62d06ab72eba6a878b5eb095d46b --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 4 (recommended) +The proportion of truncated or collapsed SFS types: 0.06349206349206349 + diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/receipt_51934466.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/receipt_51934466.json new file mode 100644 index 0000000000000000000000000000000000000000..37277ae9bac8bd019fc82184dca29b657a0443c3 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/receipt_51934466.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "a7b1b6acb1716b132db2aa2e763d769211234594dac169a39a017a58be70f070", + "elapsed_s": 168, + "failure_sha256": null, + "host": "cn604-09", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51934466", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "f0b79c126bf8c9d1ba74dba1e9db91894d04829350865c981f8bab6fc6defd34", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:24:04Z" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/submissions.jsonl b/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..bc76e2d8a161f715cd0668e0424eb3570b57097c --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g2/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g2/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_GROW_X100_300/receipts/export_51933106.json"], "job_id": "51934466", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_GROW_X100_300/fitcoal_g2.json", "request_sha256": "455bf9659a735f1980da1182f29d2de2273abde52c7872ad2cad12e12ff88c56", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [2], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "f0b79c126bf8c9d1ba74dba1e9db91894d04829350865c981f8bab6fc6defd34", "stage": "v2", "usage_before": {"account_jobs": 169, "bench_cores": 464, "bench_gpus": 17, "bench_jobs": 98, "bench_pending": 16, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:21:12Z"} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/envlock_check_51934467.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/envlock_check_51934467.json new file mode 100644 index 0000000000000000000000000000000000000000..b7a1529af02fce5167b5ff0e4987ed05710576b4 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/envlock_check_51934467.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-04", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51934467", + "status": "PASS", + "utc": "20260916T112122Z" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fit_spec.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..f37f95c163e23a4b068e74245d60743a26f1179e --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_GROW_X100_300", + "g": 3, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_GROW_X100_300/r00000003/n32" + ], + "rep": 3, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..e9db198b4339519f1d96133415f2afe0a56bfce2 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +20536 7814 5230 3724 2958 2362 2048 1847 1587 1463 1449 1283 1180 1050 1010 963 875 800 805 752 706 721 657 644 517 544 511 551 459 469 518 424 420 392 387 432 392 398 370 369 381 386 335 319 315 292 310 305 298 283 301 315 334 302 246 276 258 208 257 238 279 248 187 \ No newline at end of file diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..cd0a44a8c3a0f5ed4e45b9107e29b0b846361854 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g3/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g3/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 3 -randSeed 3 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..9a1960891eedc59380d1fd9fece631d0ef8c86d6 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 10,766 changeTypes: 0 +maxLogL = -1033.2699394025042 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 45,734 changeTypes: 2 +standardTime: 0.015585088217585426 generations: 601.32 N: 9,864 changeTypes: 0 +maxLogL = -307.38801779346386 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 205,315 changeTypes: 2 +standardTime: 0.003756094989693851 generations: 276.95 N: 12,317 changeTypes: 2 +standardTime: 0.0603352772470801 generations: 1519.50 N: 9,830 changeTypes: 0 +maxLogL = -305.28104205956424 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 45,734 changeTypes: 2 +standardTime: 0.015585088217585426 generations: 601.32 N: 9,864 changeTypes: 0 +maxLogL = -307.38801779346386 + +computing time = 132.83 seconds diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fitcoal/output.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..0c27f239b39477901e76e8a0ca7aa68f7709d6b8 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 9864 +4000000 9864 + diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..47de88aebecef4006ba97a94faaf20de764f8f92 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 3 (recommended) +The proportion of truncated or collapsed SFS types: 0.047619047619047616 + diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/receipt_51934467.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/receipt_51934467.json new file mode 100644 index 0000000000000000000000000000000000000000..d2a8af06ebd145cf4b478938f73f7316083c4f38 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/receipt_51934467.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "65bddd6f3c9c11a118dfa5afd76d0eef59cfd44505087dec60d2b78c016425c9", + "elapsed_s": 146, + "failure_sha256": null, + "host": "cn604-04", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51934467", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "25e7720a845c15c59838a911842818a9c80dd04e99c7207d975081d2d4dc47fc", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:23:46Z" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/submissions.jsonl b/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..00a82d3ca0682e77cd68c62e07d8ecdda8729765 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g3/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g3/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_GROW_X100_300/receipts/export_51933106.json"], "job_id": "51934467", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_GROW_X100_300/fitcoal_g3.json", "request_sha256": "87b173e2b1dff928d771802ae7d46552dddbd711b1c42b2211a685ca8a8f8840", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [3], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "25e7720a845c15c59838a911842818a9c80dd04e99c7207d975081d2d4dc47fc", "stage": "v2", "usage_before": {"account_jobs": 170, "bench_cores": 466, "bench_gpus": 17, "bench_jobs": 99, "bench_pending": 17, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:21:16Z"} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/envlock_check_51934479.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/envlock_check_51934479.json new file mode 100644 index 0000000000000000000000000000000000000000..141c38897b4f7de8e2913c1b3bb45155f6be209d --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/envlock_check_51934479.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-14", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51934479", + "status": "PASS", + "utc": "20260916T112130Z" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fit_spec.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..34935b0e312470ae8ded94a129a798dedb9f4c46 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_GROW_X100_300", + "g": 4, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_GROW_X100_300/r00000004/n32" + ], + "rep": 4, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..c858561f53c2c94f49cdce84bc8255683e2981b2 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +20610 7685 4968 3775 2926 2475 2255 1969 1712 1538 1350 1216 1099 1010 1067 879 899 866 800 668 697 695 663 612 640 602 611 561 557 515 451 465 480 426 421 370 377 395 410 363 344 385 347 299 272 332 303 363 369 320 256 276 260 290 285 265 275 216 213 274 213 275 257 \ No newline at end of file diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..ecad25ca5fda3ed67e0d6cd87a8261940260f964 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g4/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g4/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 2 -randSeed 4 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..3b9cc0569bfeff55bdf6faaca857d1519cfd27bf --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 10,822 changeTypes: 0 +maxLogL = -1033.635155584571 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 66,942 changeTypes: 1 +standardTime: 0.002196168274385372 generations: 294.03 N: 9,998 changeTypes: 0 +maxLogL = -324.8561463505488 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 76,670 changeTypes: 1 +standardTime: 0.0018261463393822795 generations: 280.02 N: 10,063 changeTypes: 1 +standardTime: 1.9728183146944487 generations: 39949.87 N: 9,500 changeTypes: 0 +maxLogL = -324.0361547372694 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 66,942 changeTypes: 1 +standardTime: 0.002196168274385372 generations: 294.03 N: 9,998 changeTypes: 0 +maxLogL = -324.8561463505488 + +computing time = 122.65 seconds diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fitcoal/output.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..10b0f29c441fc9d3e327ab78397e8d8b7a87eef1 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 9998 +4000000 9998 + diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..a58943a48f97b8f2d3333cf34f4a28b685cf1127 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 2 (recommended) +The proportion of truncated or collapsed SFS types: 0.031746031746031744 + diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/receipt_51934479.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/receipt_51934479.json new file mode 100644 index 0000000000000000000000000000000000000000..f6845d59ed9229d79b381c8293b7b6e29a0fadfb --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/receipt_51934479.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "d3464ef82ba29e239274830915fefeeeb079f87101d86fba09e2f3fdf8191811", + "elapsed_s": 134, + "failure_sha256": null, + "host": "cn604-14", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51934479", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "8b74b68adabaf8ab38cc6b67be77f9dd3c1c5f8c65ec212d749337e7b25ac900", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:23:42Z" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/submissions.jsonl b/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..ad10da4c3b1d9fcc8b2b93ed7fc142728c058e25 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g4/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g4/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_GROW_X100_300/receipts/export_51933106.json"], "job_id": "51934479", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_GROW_X100_300/fitcoal_g4.json", "request_sha256": "c0cc1ee6563a31553c309b38e013af153b0b05a24edac611f81415605649e98d", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [4], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "8b74b68adabaf8ab38cc6b67be77f9dd3c1c5f8c65ec212d749337e7b25ac900", "stage": "v2", "usage_before": {"account_jobs": 171, "bench_cores": 468, "bench_gpus": 17, "bench_jobs": 100, "bench_pending": 16, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:21:25Z"} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/envlock_check_51934481.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/envlock_check_51934481.json new file mode 100644 index 0000000000000000000000000000000000000000..63d4c0096715022aec9317c4d0ca6e9482b73d93 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/envlock_check_51934481.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-13", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51934481", + "status": "PASS", + "utc": "20260916T112134Z" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fit_spec.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..4ee956bd60355879ab85e7abf94445f0b78111c4 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_GROW_X100_300", + "g": 5, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_GROW_X100_300/r00000005/n32" + ], + "rep": 5, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..df30a77eb309451e0d2cf18187e9f54ea82891ad --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +20235 7511 5043 3860 2978 2509 2327 1842 1836 1538 1252 1248 1242 1186 1022 957 942 920 802 754 689 654 602 617 560 580 595 568 512 507 482 470 438 421 410 448 441 369 366 376 356 335 346 394 339 343 314 335 346 335 301 292 272 253 313 251 249 279 301 280 262 236 238 \ No newline at end of file diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..537a272b2afdc2049d4988b59bea73b9d83c7c12 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g5/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g5/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 5 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..9693c2c5650ce391aa370194fb673850dc1d2099 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 10,868 changeTypes: 0 +maxLogL = -898.3360244045277 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 117,215 changeTypes: 1 +standardTime: 0.001001708691641063 generations: 234.83 N: 10,153 changeTypes: 0 +maxLogL = -329.3383566383486 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 53,627 changeTypes: 1 +standardTime: 0.0037028859725130015 generations: 397.15 N: 4,456 changeTypes: 2 +standardTime: 0.023897983620511053 generations: 661.95 N: 10,212 changeTypes: 0 +maxLogL = -327.01843788799374 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 117,215 changeTypes: 1 +standardTime: 0.001001708691641063 generations: 234.83 N: 10,153 changeTypes: 0 +maxLogL = -329.3383566383486 + +computing time = 127.52 seconds diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fitcoal/output.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..f3c54481fc01a3e959c5226a1adc30965c3a159c --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 10153 +4000000 10153 + diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/receipt_51934481.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/receipt_51934481.json new file mode 100644 index 0000000000000000000000000000000000000000..c3d2be165de5a6dfc29203468e33a433f3d595a2 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/receipt_51934481.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "4782b6287090eadd9a8a3bda61b85ced42359d5b022582b1c7bfe4d70426e120", + "elapsed_s": 140, + "failure_sha256": null, + "host": "cn604-13", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51934481", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "f33bc26f8c71cf6e673f749740a907ba00bb9c1e7e386dd3a3927ba3a7ba9b8c", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:23:52Z" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/submissions.jsonl b/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..e54b6ac8cb4e6a04a6c6d856de18c8ae9ec32a1c --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g5/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g5/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_GROW_X100_300/receipts/export_51933106.json"], "job_id": "51934481", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_GROW_X100_300/fitcoal_g5.json", "request_sha256": "fab9d98707610a9410e1edf8a899e578f6752f5e666dc25dd2cbb1b690fd1ef3", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [5], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "f33bc26f8c71cf6e673f749740a907ba00bb9c1e7e386dd3a3927ba3a7ba9b8c", "stage": "v2", "usage_before": {"account_jobs": 171, "bench_cores": 468, "bench_gpus": 17, "bench_jobs": 100, "bench_pending": 17, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:21:27Z"} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/envlock_check_51934484.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/envlock_check_51934484.json new file mode 100644 index 0000000000000000000000000000000000000000..581766a688ebdd10d878ea1717adf71a45ca2f63 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/envlock_check_51934484.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-05", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51934484", + "status": "PASS", + "utc": "20260916T112146Z" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fit_spec.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..f176db82f490b2e5c2ebf577c81ef7f6308d7c56 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_GROW_X100_300", + "g": 6, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_GROW_X100_300/r00000006/n32" + ], + "rep": 6, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..6d3ed0f98acad6f11a7926745d86c88fac369289 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +20412 7849 5027 3593 2909 2437 2092 1795 1563 1514 1315 1223 1175 945 1075 894 842 804 809 756 672 689 662 658 571 537 572 489 505 498 547 428 450 372 349 390 356 392 384 353 384 347 366 323 334 340 339 317 328 275 296 298 344 279 250 271 261 269 242 220 228 257 204 \ No newline at end of file diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..09a677e5e82835dcd17867c5082163e8eed1e216 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g6/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g6/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 6 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..be8d15565d52f527262cf1a7c120a2ecd5bafc24 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 10,670 changeTypes: 0 +maxLogL = -1063.057274995982 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 43,994 changeTypes: 2 +standardTime: 0.016332454942264613 generations: 617.24 N: 9,768 changeTypes: 0 +maxLogL = -322.56983446679146 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 39,180 changeTypes: 2 +standardTime: 0.019263850966127167 generations: 690.31 N: 9,630 changeTypes: 2 +standardTime: 1.8005709463863468 generations: 35550.59 N: 9,944 changeTypes: 0 +maxLogL = -321.73021692664815 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 43,994 changeTypes: 2 +standardTime: 0.016332454942264613 generations: 617.24 N: 9,768 changeTypes: 0 +maxLogL = -322.56983446679146 + +computing time = 146.19 seconds diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fitcoal/output.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..0545fb99ddc5a67b365cd9a84fad745fbd72adf3 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 9768 +4000000 9768 + diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/receipt_51934484.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/receipt_51934484.json new file mode 100644 index 0000000000000000000000000000000000000000..2b4de8ed63a627a754817e13edb1f3e5c4843b66 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/receipt_51934484.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "580ef92de07a3728f4ee939eb131aaad9eddf67254f812bae0fc3b4f4e73b203", + "elapsed_s": 165, + "failure_sha256": null, + "host": "cn604-05", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51934484", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "8660e16d2e3c11c3e804450ef32ad21b3df88ea8780ee1957d14b1cd0eb14744", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:24:28Z" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/submissions.jsonl b/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..f0dd4fbdf63ff2b74448e820a97588373a958409 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g6/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g6/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_GROW_X100_300/receipts/export_51933106.json"], "job_id": "51934484", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_GROW_X100_300/fitcoal_g6.json", "request_sha256": "01c80438d0a05ac3199dffe2ffe30d0562ccce327021f09916986e5f16034a8b", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [6], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "8660e16d2e3c11c3e804450ef32ad21b3df88ea8780ee1957d14b1cd0eb14744", "stage": "v2", "usage_before": {"account_jobs": 171, "bench_cores": 462, "bench_gpus": 17, "bench_jobs": 100, "bench_pending": 16, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:21:40Z"} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/envlock_check_51934488.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/envlock_check_51934488.json new file mode 100644 index 0000000000000000000000000000000000000000..1780a24a0c180196881d6cc6f297953bf1923284 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/envlock_check_51934488.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-13", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51934488", + "status": "PASS", + "utc": "20260916T112212Z" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fit_spec.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..e78a7145041c7219eb7256ab8e9a184f4c944e73 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_GROW_X100_300", + "g": 7, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_GROW_X100_300/r00000007/n32" + ], + "rep": 7, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..13f98230fb3db3c61b7da87ca3f377c4eeee3b60 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +20099 7463 5097 3907 3034 2507 2121 1982 1753 1571 1252 1182 1072 1121 1013 969 923 871 706 698 687 659 695 577 648 515 527 487 531 490 490 432 432 409 402 425 408 444 396 387 406 390 365 348 294 315 296 355 300 294 286 269 284 286 292 310 265 258 221 285 257 216 226 \ No newline at end of file diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..4291c219eef9770e1e8a6c2889a44856c7add48b --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g7/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g7/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 1 -randSeed 7 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..0b1681dcf5e7ac3c1b05441aa049efa5b2dce513 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 10,748 changeTypes: 0 +maxLogL = -918.726057800866 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 512,940 changeTypes: 2 +standardTime: 0.004043937873648567 generations: 325.24 N: 10,018 changeTypes: 0 +maxLogL = -330.35817099329495 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 98,117 changeTypes: 1 +standardTime: 0.0013229017220147776 generations: 259.60 N: 9,364 changeTypes: 1 +standardTime: 0.018052613722122888 generations: 572.90 N: 10,032 changeTypes: 0 +maxLogL = -329.9504086395144 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 512,940 changeTypes: 2 +standardTime: 0.004043937873648567 generations: 325.24 N: 10,018 changeTypes: 0 +maxLogL = -330.35817099329495 + +computing time = 140.43 seconds diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fitcoal/output.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..e4cfce2869f007fcc6443a6e806aeba9c928f4a7 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 10018 +4000000 10018 + diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..5dc872fd79c57a0630616d4dc65b24263eb0d126 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 1 (recommended) +The proportion of truncated or collapsed SFS types: 0.015873015873015872 + diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/receipt_51934488.json b/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/receipt_51934488.json new file mode 100644 index 0000000000000000000000000000000000000000..dccfa246b0a966b5ba5b193ebf01745f6ea5e943 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/receipt_51934488.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "a545dd8f218348cc6a917f24055ffadbf4b977f8c1da585b9555ca28a6119ead", + "elapsed_s": 168, + "failure_sha256": null, + "host": "cn604-13", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51934488", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "21e73a69feaca82af210e56a03c922308f902a58b641a653638ca7ac28589105", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T11:24:40Z" +} diff --git a/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/submissions.jsonl b/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..9cc3edafe862d96e7948261308705ba6e018e2c1 --- /dev/null +++ b/estimates/fitcoal/a1/GROW_X100_300/K1/g7/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_GROW_X100_300/K1/g7/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_GROW_X100_300/receipts/export_51933106.json"], "job_id": "51934488", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_GROW_X100_300/fitcoal_g7.json", "request_sha256": "fcb861fe766602bbe5b92352eba5e5bb2e9d9c9751655daadd186713f6063b5d", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [7], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "21e73a69feaca82af210e56a03c922308f902a58b641a653638ca7ac28589105", "stage": "v2", "usage_before": {"account_jobs": 172, "bench_cores": 464, "bench_gpus": 17, "bench_jobs": 101, "bench_pending": 16, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:21:49Z"} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/envlock_check_51959990.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/envlock_check_51959990.json new file mode 100644 index 0000000000000000000000000000000000000000..869bc30f1d155ce53b8f3b4eae5914d8e00dec7f --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/envlock_check_51959990.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-17", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51959990", + "status": "PASS", + "utc": "20260916T144919Z" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fit_spec.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..c8b22ee6e40dd2d8a54350772f7066baadf8c0e9 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_S1_DroMel_African3Epoch_1S16", + "g": 0, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_S1_DroMel_African3Epoch_1S16/r00000000/n32" + ], + "rep": 0, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..7a08f98585d093f69c03aa9eecdd80dbcaf43f79 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +681612 317250 192672 133039 97636 75410 60011 48998 40705 34366 29727 25738 22886 20485 18285 16153 15037 13874 12944 12004 11339 10657 10150 9574 9263 8663 8286 7902 7763 7355 7286 6954 6689 6444 6279 6067 5917 5884 5692 5495 5333 5333 5026 5016 4741 4642 4653 4546 4376 4395 4272 3989 4088 4030 3932 3815 3810 3665 3667 3546 3471 3523 3369 \ No newline at end of file diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..e38a07d002669b1e2ff6f6912d2de70357f2078e --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g0/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g0/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 0 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..43fcee1cb29233eddec43ad45dd1cabf3cfa7c50 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 298,873 changeTypes: 0 +maxLogL = -185564.7752485096 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 503,345 changeTypes: 1 +standardTime: 0.20086108167763067 generations: 202204.70 N: 144,172 changeTypes: 0 +maxLogL = -449.8220901753775 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 362,633 changeTypes: 2 +standardTime: 0.004933099226273474 generations: 4241.97 N: 515,013 changeTypes: 1 +standardTime: 0.1930991293166335 generations: 198057.91 N: 144,937 changeTypes: 0 +maxLogL = -385.02228920639027 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 503,345 changeTypes: 1 +standardTime: 0.20086108167763067 generations: 202204.70 N: 144,172 changeTypes: 0 +maxLogL = -449.8220901753775 + +computing time = 183.58 seconds diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fitcoal/output.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..efecf19e371cf84c6e1e8954ab1a5d0f9f8e5425 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 503345 +202205 503345 +202205 144172 +4000000 144172 + diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/receipt_51959990.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/receipt_51959990.json new file mode 100644 index 0000000000000000000000000000000000000000..455c04b7440b637d6f89e656fe174d45bfb86ac1 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/receipt_51959990.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "55440a70276cc33da5a50338fbf016abb14b37b86b2d279e4421067bcccc900f", + "elapsed_s": 228, + "failure_sha256": null, + "host": "cn604-17", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51959990", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "eed6765fa84e4de86a38124976b31fdebd7e1c05835d9ab3694624cc6b4d0d12", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T14:52:31Z" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/submissions.jsonl b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..8d5957fda73e76b4a948dc2cdfe97f61361a1901 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g0/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g0/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_S1_DroMel_African3Epoch_1S16/receipts/export_51959168.json"], "job_id": "51959990", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_S1_DroMel_African3Epoch_1S16/fitcoal_g0.json", "request_sha256": "978f8254da00dd10a880a94de0b3af077b5fc9aebe1b0ba76751bd1a09598770", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [0], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "eed6765fa84e4de86a38124976b31fdebd7e1c05835d9ab3694624cc6b4d0d12", "stage": "v2", "usage_before": {"account_jobs": 37, "bench_cores": 100, "bench_gpus": 19, "bench_jobs": 22, "bench_pending": 1, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T14:48:03Z"} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/envlock_check_51959991.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/envlock_check_51959991.json new file mode 100644 index 0000000000000000000000000000000000000000..c133d22f32f0c84dda103cbb900661a902abfa32 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/envlock_check_51959991.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-17", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51959991", + "status": "PASS", + "utc": "20260916T144925Z" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fit_spec.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..1ea53ab0523d7c90beb333eeb5e94a1ed4242217 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_S1_DroMel_African3Epoch_1S16", + "g": 1, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_S1_DroMel_African3Epoch_1S16/r00000001/n32" + ], + "rep": 1, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..588b4255f6d6f53a365ab979ad45eae54cc7bd4f --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +682288 317117 193897 132945 98800 75496 59965 49439 41124 34195 29632 25834 22696 20013 18256 16466 15208 13868 12809 12439 11320 10535 10161 9516 9086 8594 8378 8023 7701 7241 6902 6679 6511 6428 6235 6065 6044 5680 5509 5493 5242 5096 4995 5065 4813 4606 4676 4354 4376 4231 4274 4151 4077 4130 3940 3898 3820 3618 3780 3641 3484 3402 3400 \ No newline at end of file diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..b297eb596f615dda9d30d31913d228ae19a7adf5 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g1/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g1/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 1 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..1c4fcf33da53765539da495b8c50a1cce56b7c22 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 299,145 changeTypes: 0 +maxLogL = -187203.15088903846 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 503,526 changeTypes: 1 +standardTime: 0.20313736619787223 generations: 204569.88 N: 143,154 changeTypes: 0 +maxLogL = -466.8319856968192 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 477,390 changeTypes: 2 +standardTime: 0.12943919411238142 generations: 138206.24 N: 599,611 changeTypes: 2 +standardTime: 0.30233663844208036 generations: 231612.95 N: 143,817 changeTypes: 0 +maxLogL = -396.5298509635868 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 503,526 changeTypes: 1 +standardTime: 0.20313736619787223 generations: 204569.88 N: 143,154 changeTypes: 0 +maxLogL = -466.8319856968192 + +computing time = 215.28 seconds diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fitcoal/output.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..2f6dc30ef4aee303cb510a1e48b93bcf2593dd0c --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 503526 +204570 503526 +204570 143154 +4000000 143154 + diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/receipt_51959991.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/receipt_51959991.json new file mode 100644 index 0000000000000000000000000000000000000000..4a8ee15ddbe0f80dad15d48a8e64d11195d4d2d9 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/receipt_51959991.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "2b95dbd35575080b3d47dbda1887a050d3c4fa583cc2c2cd38584c5500a6827f", + "elapsed_s": 265, + "failure_sha256": null, + "host": "cn604-17", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51959991", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "7af25e84970396b1c971c25737dbf3fa4d89298540f228d286da45bf61a3ffd1", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T14:53:08Z" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/submissions.jsonl b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..aeb5926c9c5f343bc3324504172a697d3c145cac --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g1/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g1/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_S1_DroMel_African3Epoch_1S16/receipts/export_51959168.json"], "job_id": "51959991", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_S1_DroMel_African3Epoch_1S16/fitcoal_g1.json", "request_sha256": "ccb739a7ba8901e3be2029c237c6dd81bd0212e16b053fc2caf1e8476499e933", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [1], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "7af25e84970396b1c971c25737dbf3fa4d89298540f228d286da45bf61a3ffd1", "stage": "v2", "usage_before": {"account_jobs": 38, "bench_cores": 102, "bench_gpus": 19, "bench_jobs": 23, "bench_pending": 2, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T14:48:05Z"} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/envlock_check_51959992.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/envlock_check_51959992.json new file mode 100644 index 0000000000000000000000000000000000000000..c28186be961f928325506f09fa12a66e347b8206 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/envlock_check_51959992.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-17", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51959992", + "status": "PASS", + "utc": "20260916T144925Z" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fit_spec.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..37b7c7357be00e3c003ab3cbb9b4290dc910906d --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_S1_DroMel_African3Epoch_1S16", + "g": 2, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_S1_DroMel_African3Epoch_1S16/r00000002/n32" + ], + "rep": 2, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..e80fff610ca6316387343176d731a985e7415cb2 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +684622 314959 193339 133194 98147 75542 60738 48855 40072 34363 29499 25983 22671 20335 18443 16409 15211 13871 12688 11953 11406 10761 9813 9687 9037 8722 8339 7914 7742 7262 7115 6935 6585 6335 6391 6153 5822 5843 5756 5545 5357 5158 4975 4989 4796 4687 4511 4602 4522 4253 4079 4070 4001 4001 4002 3813 3827 3601 3650 3700 3510 3454 3328 \ No newline at end of file diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..c1ae7164ce832225fbf9f6bd21866cbb5be750c4 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g2/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g2/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 1 -randSeed 2 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..61b2937e67fbb01bbb2f241051cb0a964213366c --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 299,581 changeTypes: 0 +maxLogL = -185758.24962655533 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 504,361 changeTypes: 1 +standardTime: 0.20079248924486415 generations: 202543.96 N: 143,768 changeTypes: 0 +maxLogL = -436.033761358849 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 493,780 changeTypes: 1 +standardTime: 0.09053612716214751 generations: 89409.90 N: 957,159 changeTypes: 2 +standardTime: 0.3169720443778784 generations: 234995.30 N: 144,284 changeTypes: 0 +maxLogL = -391.8986893908841 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 504,361 changeTypes: 1 +standardTime: 0.20079248924486415 generations: 202543.96 N: 143,768 changeTypes: 0 +maxLogL = -436.033761358849 + +computing time = 221.08 seconds diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fitcoal/output.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..df33eff26cbe60979b187aba8a2761dc220890dc --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 504361 +202544 504361 +202544 143768 +4000000 143768 + diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..5dc872fd79c57a0630616d4dc65b24263eb0d126 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 1 (recommended) +The proportion of truncated or collapsed SFS types: 0.015873015873015872 + diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/receipt_51959992.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/receipt_51959992.json new file mode 100644 index 0000000000000000000000000000000000000000..303097a599ea0ad0cb7c770fb751a0bf2d2323dc --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/receipt_51959992.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "a2438ee190d587c51085ca334d15e332565288da40a4478e738f66637c60fe37", + "elapsed_s": 272, + "failure_sha256": null, + "host": "cn604-17", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51959992", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "30bc8f1663c5374dd0efd23549ef80f571d3845ee5970d24d69912b87703faf1", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T14:53:15Z" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/submissions.jsonl b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..2317fa5152e90b779d82b5522f789e18c504d35d --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g2/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g2/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_S1_DroMel_African3Epoch_1S16/receipts/export_51959168.json"], "job_id": "51959992", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_S1_DroMel_African3Epoch_1S16/fitcoal_g2.json", "request_sha256": "bcbd5d47fb98dab3fdcec59b4e1913da88bf1a8b559b6f7e4345b2a39e900a13", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [2], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "30bc8f1663c5374dd0efd23549ef80f571d3845ee5970d24d69912b87703faf1", "stage": "v2", "usage_before": {"account_jobs": 39, "bench_cores": 104, "bench_gpus": 19, "bench_jobs": 24, "bench_pending": 3, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T14:48:07Z"} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/envlock_check_51959993.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/envlock_check_51959993.json new file mode 100644 index 0000000000000000000000000000000000000000..c76eee651cfe946ea04361a634e644e8acbb7cc9 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/envlock_check_51959993.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-17", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51959993", + "status": "PASS", + "utc": "20260916T144855Z" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fit_spec.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..96ee415a4ebc8009be23db3b3fb7078526f58b60 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_S1_DroMel_African3Epoch_1S16", + "g": 3, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_S1_DroMel_African3Epoch_1S16/r00000003/n32" + ], + "rep": 3, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..074ca5442c97ebc5f1d4db9c9584a15d458108b7 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +681474 316761 193646 133428 97355 75570 59720 48374 40476 34479 29520 25753 22781 19988 17865 16496 15289 13867 12994 12123 11207 10732 10011 9282 8925 8701 8350 8057 7698 7470 7193 6834 6686 6288 6124 6096 5925 5723 5679 5449 5275 5145 5013 4837 4812 4677 4563 4525 4487 4333 4318 4029 4068 4033 3922 4096 3780 3703 3518 3698 3616 3551 3343 \ No newline at end of file diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..8effb42cef48b87a1a0e76839b60d60f56544e2a --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g3/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g3/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 1 -randSeed 3 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..9830cad8abb616dad7e77baad70a327c189b70b7 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 299,124 changeTypes: 0 +maxLogL = -185402.281906027 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 503,928 changeTypes: 1 +standardTime: 0.19998630682913118 generations: 201557.31 N: 143,780 changeTypes: 0 +maxLogL = -467.82855287471466 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 453,524 changeTypes: 2 +standardTime: 0.022217001304507385 generations: 21609.04 N: 522,351 changeTypes: 1 +standardTime: 0.18893459621825262 generations: 195779.12 N: 144,823 changeTypes: 0 +maxLogL = -384.2284139340518 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 458,196 changeTypes: 2 +standardTime: 0.026713725198208835 generations: 26175.98 N: 524,674 changeTypes: 1 +standardTime: 0.18642190484307497 generations: 193765.53 N: 148,766 changeTypes: 2 +standardTime: 0.7190675380332994 generations: 349961.97 N: 144,521 changeTypes: 0 +maxLogL = -384.02790007555814 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 453,524 changeTypes: 2 +standardTime: 0.022217001304507385 generations: 21609.04 N: 522,351 changeTypes: 1 +standardTime: 0.18893459621825262 generations: 195779.12 N: 144,823 changeTypes: 0 +maxLogL = -384.2284139340518 + +computing time = 642.91 seconds diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fitcoal/output.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..2cc5fe33712a33f55bcc3ed4427dd279032a02c3 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fitcoal/output.txt @@ -0,0 +1,106 @@ +year popSize +2000 459494 +2196 460083 +2392 460673 +2588 461264 +2784 461856 +2980 462449 +3177 463042 +3373 463636 +3569 464231 +3765 464826 +3961 465423 +4157 466020 +4353 466618 +4549 467217 +4745 467816 +4941 468416 +5137 469017 +5334 469619 +5530 470221 +5726 470825 +5922 471429 +6118 472033 +6314 472639 +6510 473245 +6706 473853 +6902 474461 +7098 475069 +7294 475679 +7491 476289 +7687 476900 +7883 477512 +8079 478125 +8275 478738 +8471 479352 +8667 479967 +8863 480583 +9059 481200 +9255 481817 +9451 482435 +9648 483054 +9844 483674 +10040 484294 +10236 484916 +10432 485538 +10628 486161 +10824 486784 +11020 487409 +11216 488034 +11412 488660 +11608 489287 +11805 489915 +12001 490544 +12197 491173 +12393 491803 +12589 492434 +12785 493066 +12981 493698 +13177 494332 +13373 494966 +13569 495601 +13765 496237 +13962 496874 +14158 497511 +14354 498149 +14550 498788 +14746 499428 +14942 500069 +15138 500711 +15334 501353 +15530 501996 +15726 502640 +15922 503285 +16119 503931 +16315 504577 +16511 505225 +16707 505873 +16903 506522 +17099 507172 +17295 507822 +17491 508474 +17687 509126 +17883 509780 +18079 510434 +18275 511088 +18472 511744 +18668 512401 +18864 513058 +19060 513716 +19256 514375 +19452 515035 +19648 515696 +19844 516358 +20040 517020 +20236 517684 +20432 518348 +20629 519013 +20825 519679 +21021 520345 +21217 521013 +21413 521681 +21609 522351 +195779 522351 +195779 144823 +4000000 144823 + diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..5dc872fd79c57a0630616d4dc65b24263eb0d126 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 1 (recommended) +The proportion of truncated or collapsed SFS types: 0.015873015873015872 + diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/receipt_51959993.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/receipt_51959993.json new file mode 100644 index 0000000000000000000000000000000000000000..c65eb06ca27c4b1ae61af101f1ff8ad416e61ee5 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/receipt_51959993.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "b80cb264727947594686fd270b8fe4ec28eb54ac6b79f00610e5fa7f49f8f70a", + "elapsed_s": 667, + "failure_sha256": null, + "host": "cn604-17", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51959993", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "4e086d9a71b63f9504648585a221365bf026782ce121db2d5bdf646b49ee380b", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T14:59:50Z" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/submissions.jsonl b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..692176110fd8bf31ed1853599b15d15d4f306305 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g3/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g3/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_S1_DroMel_African3Epoch_1S16/receipts/export_51959168.json"], "job_id": "51959993", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_S1_DroMel_African3Epoch_1S16/fitcoal_g3.json", "request_sha256": "f4034e78a78b4926ecfab69ac04e94ae59a481baa8726aff5ec186db2515d7a7", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [3], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "4e086d9a71b63f9504648585a221365bf026782ce121db2d5bdf646b49ee380b", "stage": "v2", "usage_before": {"account_jobs": 40, "bench_cores": 106, "bench_gpus": 19, "bench_jobs": 25, "bench_pending": 4, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T14:48:08Z"} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/envlock_check_51959994.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/envlock_check_51959994.json new file mode 100644 index 0000000000000000000000000000000000000000..83f884f64d3a17ddc5c1f5954e9752aa2dc206f9 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/envlock_check_51959994.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-17", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51959994", + "status": "PASS", + "utc": "20260916T144900Z" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fit_spec.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..9b3c9d10d505b5d3bfacb0f3b896a76321c7262b --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_S1_DroMel_African3Epoch_1S16", + "g": 4, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_S1_DroMel_African3Epoch_1S16/r00000004/n32" + ], + "rep": 4, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..d4b70d6d890db26804ba6a66e81d6ef28b606cad --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +680856 315367 194205 133322 97721 76001 60459 48508 40377 34183 29529 25614 23024 20152 18273 16679 14951 13794 13069 11779 11292 10699 10021 9533 8762 8589 8182 7992 7669 7358 7218 6880 6778 6407 6258 6162 6077 5796 5555 5489 5369 5303 4934 4944 4962 4893 4713 4699 4383 4421 4480 4194 4174 3977 3934 3862 3716 3744 3797 3566 3524 3441 3491 \ No newline at end of file diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..f4d4f1d4e6ed8ef267ead92d20bea4917aee5b60 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g4/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g4/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 4 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..6d7ce15d6d5be933d1d3e359a94a532eed1728f6 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 298,785 changeTypes: 0 +maxLogL = -185037.6873822717 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 503,182 changeTypes: 1 +standardTime: 0.20037794425315142 generations: 201653.22 N: 144,428 changeTypes: 0 +maxLogL = -496.9407711767017 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 476,638 changeTypes: 2 +standardTime: 0.08956284800520206 generations: 91705.44 N: 550,863 changeTypes: 1 +standardTime: 0.18080819806087683 generations: 192232.90 N: 145,894 changeTypes: 0 +maxLogL = -399.9393120356799 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 480,408 changeTypes: 1 +standardTime: 0.027654079790917725 generations: 26570.47 N: 526,217 changeTypes: 1 +standardTime: 0.20042267244924897 generations: 208398.07 N: 56,438 changeTypes: 1 +standardTime: 0.26310524500343113 generations: 215473.48 N: 146,162 changeTypes: 0 +maxLogL = -399.24907242654444 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 476,638 changeTypes: 2 +standardTime: 0.08956284800520206 generations: 91705.44 N: 550,863 changeTypes: 1 +standardTime: 0.18080819806087683 generations: 192232.90 N: 145,894 changeTypes: 0 +maxLogL = -399.9393120356799 + +computing time = 646.12 seconds diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fitcoal/output.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..df5aa4bf252228d90f2e64c4a62250d49aef1c38 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fitcoal/output.txt @@ -0,0 +1,106 @@ +year popSize +2000 478145 +2897 478822 +3794 479500 +4691 480180 +5588 480860 +6485 481541 +7382 482223 +8279 482907 +9176 483591 +10073 484276 +10971 484962 +11868 485649 +12765 486337 +13662 487026 +14559 487716 +15456 488407 +16353 489099 +17250 489792 +18147 490486 +19044 491181 +19941 491877 +20838 492574 +21735 493271 +22632 493970 +23529 494670 +24426 495371 +25323 496073 +26220 496775 +27118 497479 +28015 498184 +28912 498890 +29809 499597 +30706 500304 +31603 501013 +32500 501723 +33397 502434 +34294 503146 +35191 503859 +36088 504572 +36985 505287 +37882 506003 +38779 506720 +39676 507438 +40573 508157 +41470 508877 +42367 509598 +43265 510320 +44162 511043 +45059 511767 +45956 512492 +46853 513218 +47750 513945 +48647 514673 +49544 515402 +50441 516132 +51338 516863 +52235 517596 +53132 518329 +54029 519063 +54926 519799 +55823 520535 +56720 521273 +57617 522011 +58514 522751 +59411 523491 +60309 524233 +61206 524976 +62103 525719 +63000 526464 +63897 527210 +64794 527957 +65691 528705 +66588 529454 +67485 530204 +68382 530955 +69279 531707 +70176 532461 +71073 533215 +71970 533971 +72867 534727 +73764 535485 +74661 536243 +75558 537003 +76456 537764 +77353 538526 +78250 539289 +79147 540053 +80044 540818 +80941 541584 +81838 542351 +82735 543120 +83632 543889 +84529 544660 +85426 545431 +86323 546204 +87220 546978 +88117 547753 +89014 548529 +89911 549306 +90808 550084 +91705 550863 +192233 550863 +192233 145894 +4000000 145894 + diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/receipt_51959994.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/receipt_51959994.json new file mode 100644 index 0000000000000000000000000000000000000000..d1b118eb3182297e4e755dec10a1410d594b51b1 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/receipt_51959994.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "f50a346b88da25f3f8846fa41542d54d97fb0a1b661a5a75715ade308a701edc", + "elapsed_s": 671, + "failure_sha256": null, + "host": "cn604-17", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51959994", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "037a08a40cae60a5dd7308cdabcabba908145a31e4fd41d6e23468a0243f1de6", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T14:59:54Z" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/submissions.jsonl b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..01ceaab88530c964f6a678fec5662adbd79f3c66 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g4/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g4/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_S1_DroMel_African3Epoch_1S16/receipts/export_51959168.json"], "job_id": "51959994", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_S1_DroMel_African3Epoch_1S16/fitcoal_g4.json", "request_sha256": "5a8968b17b27d31c5acddcb0400a196853bcd0fe4a222ca3dd8cd952561189de", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [4], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "037a08a40cae60a5dd7308cdabcabba908145a31e4fd41d6e23468a0243f1de6", "stage": "v2", "usage_before": {"account_jobs": 41, "bench_cores": 108, "bench_gpus": 19, "bench_jobs": 26, "bench_pending": 5, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T14:48:10Z"} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/envlock_check_51959996.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/envlock_check_51959996.json new file mode 100644 index 0000000000000000000000000000000000000000..628f6a7745ac5721527b72f16919e5ac1d5a9ad8 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/envlock_check_51959996.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-17", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51959996", + "status": "PASS", + "utc": "20260916T144857Z" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fit_spec.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..b88a36636e215b4c0d9b5019f6ca66ccdb98a439 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_S1_DroMel_African3Epoch_1S16", + "g": 5, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_S1_DroMel_African3Epoch_1S16/r00000005/n32" + ], + "rep": 5, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..5e58dc705e630063cedf58c80467649a049edea5 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +682290 315292 194337 133678 97665 75452 60084 49280 40996 34495 29648 26290 22703 20232 18097 16558 15106 13949 12833 12153 11196 10436 9886 9386 9053 8676 8274 8019 7652 7397 7060 6685 6690 6255 6096 6177 5941 5689 5586 5437 5140 5221 4908 5039 4874 4743 4654 4640 4403 4374 4391 4281 4157 4077 4078 3749 3861 3687 3741 3535 3387 3492 3344 \ No newline at end of file diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..430517075fafa09d4d07a6dcc74c194e6a983941 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g5/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g5/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 5 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..decd3cc6c89fc29a03ab3a4e17981f245fedb47f --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 298,983 changeTypes: 0 +maxLogL = -186419.56853196502 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 503,011 changeTypes: 1 +standardTime: 0.20291275736181918 generations: 204134.60 N: 143,394 changeTypes: 0 +maxLogL = -460.1104983986079 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 481,133 changeTypes: 2 +standardTime: 0.08077320590182002 generations: 82013.21 N: 536,208 changeTypes: 1 +standardTime: 0.18780399133513212 generations: 196794.68 N: 144,562 changeTypes: 0 +maxLogL = -397.3517390280758 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 503,011 changeTypes: 1 +standardTime: 0.20291275736181918 generations: 204134.60 N: 143,394 changeTypes: 0 +maxLogL = -460.1104983986079 + +computing time = 220.65 seconds diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fitcoal/output.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..686599cce8d6fcb9979622118ef6fd2e67b7f86c --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fitcoal/output.txt @@ -0,0 +1,6 @@ +year popSize +2000 503011 +204135 503011 +204135 143394 +4000000 143394 + diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/receipt_51959996.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/receipt_51959996.json new file mode 100644 index 0000000000000000000000000000000000000000..0d2eff3e57ed5f6a1832f4b94b7f22a0dfa59989 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/receipt_51959996.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "64825e8c9c808d454df809082fa97b3b37146fcda280f37d78b924962d5ca202", + "elapsed_s": 245, + "failure_sha256": null, + "host": "cn604-17", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51959996", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "84988294062d1ad60f81c1f3e08b78b5ba42a59cac1ab8e19818f673481bee35", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T14:52:48Z" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/submissions.jsonl b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..2d16dfe835c88f44adb5e6f4e19ccfbb364a5a57 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g5/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g5/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_S1_DroMel_African3Epoch_1S16/receipts/export_51959168.json"], "job_id": "51959996", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_S1_DroMel_African3Epoch_1S16/fitcoal_g5.json", "request_sha256": "7abe608beb1a65dd32d7c964a6f50f461945c4528d2faad8e935ac99efae1566", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [5], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "84988294062d1ad60f81c1f3e08b78b5ba42a59cac1ab8e19818f673481bee35", "stage": "v2", "usage_before": {"account_jobs": 42, "bench_cores": 110, "bench_gpus": 19, "bench_jobs": 27, "bench_pending": 6, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T14:48:12Z"} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/envlock_check_51959997.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/envlock_check_51959997.json new file mode 100644 index 0000000000000000000000000000000000000000..6d1f43773dca3556d27ea1f05a3dcd629d2857bc --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/envlock_check_51959997.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-15", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51959997", + "status": "PASS", + "utc": "20260916T144910Z" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/fit_spec.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..28966878540c0caa2c5f681aa8207c095e095890 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_S1_DroMel_African3Epoch_1S16", + "g": 6, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_S1_DroMel_African3Epoch_1S16/r00000006/n32" + ], + "rep": 6, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..17e49bc6814a72a3dbf1b3d2456f865a2282321e --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +680042 316399 193369 132838 98605 75464 60259 49298 40468 34330 29604 25957 22544 20046 18182 16400 15059 13797 12868 12146 11302 10706 10001 9457 9191 8443 8234 7906 7873 7343 7167 6899 6788 6472 6315 6092 5771 5600 5627 5425 5471 5171 5062 4954 4654 4673 4601 4727 4501 4391 4363 4049 3989 3837 3880 3843 3868 3736 3636 3400 3456 3505 3394 \ No newline at end of file diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..3ba9adca03864058c2d8811c5f18f65ab8cd91fa --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g6/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g6/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 6 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..ff86e5da9a75599d0769dc293ebbf4f4e344bbd9 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 298,552 changeTypes: 0 +maxLogL = -185864.18722597178 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 502,233 changeTypes: 1 +standardTime: 0.20267701785825892 generations: 203582.16 N: 143,368 changeTypes: 0 +maxLogL = -489.7130555167896 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 474,619 changeTypes: 2 +standardTime: 0.13270918841122867 generations: 141872.60 N: 604,950 changeTypes: 2 +standardTime: 0.2870374637075139 generations: 225705.31 N: 144,300 changeTypes: 0 +maxLogL = -402.8905620531441 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 476,541 changeTypes: 2 +standardTime: 0.16887713963851336 generations: 184025.05 N: 626,860 changeTypes: 2 +standardTime: 0.17888070665831862 generations: 189657.29 N: 149,587 changeTypes: 1 +standardTime: 1.9381724907567246 generations: 715991.58 N: 132,158 changeTypes: 0 +maxLogL = -398.57524053515954 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 474,619 changeTypes: 2 +standardTime: 0.13270918841122867 generations: 141872.60 N: 604,950 changeTypes: 2 +standardTime: 0.2870374637075139 generations: 225705.31 N: 144,300 changeTypes: 0 +maxLogL = -402.8905620531441 + +computing time = 687.12 seconds diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/fitcoal/output.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..eb244f7d8d5778d36858270238a97c1b1f073f30 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/fitcoal/output.txt @@ -0,0 +1,204 @@ +year popSize +2000 476245 +3399 477386 +4797 478529 +6196 479675 +7595 480824 +8994 481976 +10392 483130 +11791 484287 +13190 485447 +14589 486609 +15987 487775 +17386 488943 +18785 490114 +20183 491288 +21582 492465 +22981 493644 +24380 494826 +25778 496011 +27177 497199 +28576 498390 +29975 499584 +31373 500780 +32772 501980 +34171 503182 +35569 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b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/receipt_51959997.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/receipt_51959997.json new file mode 100644 index 0000000000000000000000000000000000000000..90f248cf4bba2fc3c621915c1ab7434527f713a9 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/receipt_51959997.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "f5348ecc703b2337a7bd0f787513b10c805d465628d66cd0ca73bcd03c289fe6", + "elapsed_s": 725, + "failure_sha256": null, + "host": "cn604-15", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51959997", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "dc6b92dd9a1e7b1bbd8c63b3db662ad4ae5f3c2f11141c042b9a26654fe7323a", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T15:00:48Z" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/submissions.jsonl b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..dd6277925965d0b39b68ff9fd8ffd9de2d1836ce --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g6/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g6/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_S1_DroMel_African3Epoch_1S16/receipts/export_51959168.json"], "job_id": "51959997", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_S1_DroMel_African3Epoch_1S16/fitcoal_g6.json", "request_sha256": "e8885dc35101f023a84be97f6d0bf44fcb224ff3c35e7e00b37e8337c9d0d839", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [6], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "dc6b92dd9a1e7b1bbd8c63b3db662ad4ae5f3c2f11141c042b9a26654fe7323a", "stage": "v2", "usage_before": {"account_jobs": 43, "bench_cores": 112, "bench_gpus": 19, "bench_jobs": 28, "bench_pending": 7, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T14:48:14Z"} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/envlock_check_51959998.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/envlock_check_51959998.json new file mode 100644 index 0000000000000000000000000000000000000000..ede082e7ade9f95e751ea8361a1d88a6ec544e4d --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/envlock_check_51959998.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn604-15", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51959998", + "status": "PASS", + "utc": "20260916T144908Z" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fit_spec.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..b041f0538eb5c322b9c574d5e337a975b3ba165d --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_S1_DroMel_African3Epoch_1S16", + "g": 7, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_S1_DroMel_African3Epoch_1S16/r00000007/n32" + ], + "rep": 7, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..77f057b6f105f87db28368f44cab53654999ef03 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +684599 316729 195238 133432 97634 75314 59559 48364 40421 34780 29754 25911 22201 20173 17998 16128 14946 13792 12725 11707 11049 10705 10071 9535 8890 8723 8110 7915 7578 7165 6982 6850 6757 6410 6373 6167 6036 5869 5634 5478 5523 5143 4942 4936 4834 4650 4572 4482 4263 4265 4284 4188 4023 4024 3908 3878 3905 3878 3655 3583 3453 3403 3315 \ No newline at end of file diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..9b722592afdf93a2adf6e809cea234dc20770bfb --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g7/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g7/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 7 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..6a8f4220f7cfeab57ce6456e29d75de7c9f30b80 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fitcoal/decoder.out @@ -0,0 +1,31 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 299,026 changeTypes: 0 +maxLogL = -189427.23398052063 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 506,585 changeTypes: 1 +standardTime: 0.19873573340649645 generations: 201353.01 N: 143,278 changeTypes: 0 +maxLogL = -499.79788652754723 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 473,094 changeTypes: 2 +standardTime: 0.04629638272829488 generations: 46498.99 N: 533,717 changeTypes: 1 +standardTime: 0.18472804031926593 generations: 194265.76 N: 144,489 changeTypes: 0 +maxLogL = -410.8680026161055 + +numOfIntervals = 4 +standardTime: 0.0 generations: 0.00 N: 477,181 changeTypes: 1 +standardTime: 0.018720970258334968 generations: 17866.59 N: 525,242 changeTypes: 1 +standardTime: 0.20075678073321804 generations: 209092.25 N: 7,555 changeTypes: 1 +standardTime: 0.24033355237611048 generations: 209690.27 N: 144,717 changeTypes: 0 +maxLogL = -410.11368967971066 + +******** Best: ******** +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 473,094 changeTypes: 2 +standardTime: 0.04629638272829488 generations: 46498.99 N: 533,717 changeTypes: 1 +standardTime: 0.18472804031926593 generations: 194265.76 N: 144,489 changeTypes: 0 +maxLogL = -410.8680026161055 + +computing time = 688.17 seconds diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fitcoal/output.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..18bf98ee83ec90fa7fea205b5dbe603a7ae23d6d --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fitcoal/output.txt @@ -0,0 +1,106 @@ +year popSize +2000 475554 +2445 476103 +2890 476653 +3335 477203 +3780 477754 +4225 478306 +4670 478858 +5115 479411 +5560 479964 +6005 480518 +6450 481073 +6895 481628 +7340 482184 +7785 482741 +8230 483299 +8675 483857 +9120 484415 +9565 484974 +10010 485534 +10455 486095 +10900 486656 +11345 487218 +11790 487780 +12235 488344 +12680 488907 +13125 489472 +13570 490037 +14015 490603 +14460 491169 +14905 491736 +15350 492304 +15795 492872 +16240 493441 +16685 494011 +17130 494581 +17575 495152 +18020 495724 +18465 496296 +18910 496869 +19355 497443 +19800 498017 +20245 498592 +20690 499168 +21135 499744 +21580 500321 +22025 500899 +22470 501477 +22915 502056 +23360 502636 +23805 503216 +24249 503797 +24694 504379 +25139 504961 +25584 505544 +26029 506128 +26474 506712 +26919 507297 +27364 507883 +27809 508469 +28254 509056 +28699 509644 +29144 510232 +29589 510821 +30034 511411 +30479 512001 +30924 512593 +31369 513184 +31814 513777 +32259 514370 +32704 514964 +33149 515558 +33594 516154 +34039 516750 +34484 517346 +34929 517943 +35374 518541 +35819 519140 +36264 519739 +36709 520340 +37154 520940 +37599 521542 +38044 522144 +38489 522747 +38934 523350 +39379 523954 +39824 524559 +40269 525165 +40714 525771 +41159 526378 +41604 526986 +42049 527594 +42494 528204 +42939 528813 +43384 529424 +43829 530035 +44274 530647 +44719 531260 +45164 531873 +45609 532487 +46054 533102 +46499 533717 +194266 533717 +194266 144489 +4000000 144489 + diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/receipt_51959998.json b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/receipt_51959998.json new file mode 100644 index 0000000000000000000000000000000000000000..a9d42c53f0e9dd47defe56bd488ae8b8346cdc96 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/receipt_51959998.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "047dd3c99451386e721f0dad7a62bc96d3f9fbf3f488cbb5166648c3cca806c2", + "elapsed_s": 726, + "failure_sha256": null, + "host": "cn604-15", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51959998", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "53010aceeb12efe5292160daa0deb248115160e33852bbb8425264668181b1ff", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T15:00:49Z" +} diff --git a/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/submissions.jsonl b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..f643af3afc23b504953a3bbc7fd5da71a682e100 --- /dev/null +++ b/estimates/fitcoal/a1/S1_DroMel_African3Epoch_1S16/K1/g7/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_S1_DroMel_African3Epoch_1S16/K1/g7/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_S1_DroMel_African3Epoch_1S16/receipts/export_51959168.json"], "job_id": "51959998", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_S1_DroMel_African3Epoch_1S16/fitcoal_g7.json", "request_sha256": "4a07f0a31f77c99e93bf87c34c6fc12861bb50212c1707ad6cb760021a7e55d9", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [7], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "53010aceeb12efe5292160daa0deb248115160e33852bbb8425264668181b1ff", "stage": "v2", "usage_before": {"account_jobs": 44, "bench_cores": 114, "bench_gpus": 19, "bench_jobs": 29, "bench_pending": 8, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T14:48:15Z"} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/envlock_check_51936580.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/envlock_check_51936580.json new file mode 100644 index 0000000000000000000000000000000000000000..0a97b09d284d1cea01d9090d9c3b1519f9c0e177 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/envlock_check_51936580.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn603-26-r", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51936580", + "status": "PASS", + "utc": "20260916T120901Z" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fit_spec.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..40badb15ea39d0652512f400e13c6e9551ce5c7b --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_STEP_DOWN_X10_1K", + "g": 0, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_STEP_DOWN_X10_1K/r00000000/n32" + ], + "rep": 0, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..023cbe4fc07c0f884af5b43379a1f867e9b8ba19 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +23208 17317 14092 13052 11174 10182 9112 8111 7494 6538 6458 5927 5674 5070 4506 4477 3933 3993 4030 3698 3474 3305 3332 2864 3226 2893 2877 2804 2686 2514 2503 2244 2198 2276 2166 2070 2185 1913 2016 1904 1811 1687 1781 1735 1715 1495 1606 1572 1494 1469 1384 1504 1346 1431 1393 1382 1303 1335 1254 1278 1088 1084 1135 \ No newline at end of file diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..d2cec001bbb599d7637d1a03a3f9dc1d9b6db418 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g0/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g0/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 1 -randSeed 0 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..7b3c1f0067c579d4bd67916e6ef605f79f012e76 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 35,600 changeTypes: 0 +maxLogL = -20423.258946249844 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 4,912 changeTypes: 2 +standardTime: 0.12925927087470174 generations: 3258.70 N: 49,587 changeTypes: 0 +maxLogL = -455.0412090974314 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 5,186 changeTypes: 1 +standardTime: 0.08940622662870776 generations: 927.35 N: 43,502 changeTypes: 1 +standardTime: 0.3057613004609567 generations: 19751.28 N: 50,069 changeTypes: 0 +maxLogL = -446.8895473416678 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 4,912 changeTypes: 2 +standardTime: 0.12925927087470174 generations: 3258.70 N: 49,587 changeTypes: 0 +maxLogL = -455.0412090974314 + +computing time = 351.53 seconds diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fitcoal/output.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..b3c047b6be2fd3df35068ad62075cd8254d8df0d --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fitcoal/output.txt @@ -0,0 +1,104 @@ +year popSize +2000 20301 +2013 20483 +2025 20667 +2038 20852 +2050 21039 +2063 21228 +2076 21419 +2088 21611 +2101 21805 +2113 22000 +2126 22198 +2138 22397 +2151 22598 +2164 22800 +2176 23005 +2189 23211 +2201 23419 +2214 23630 +2227 23841 +2239 24055 +2252 24271 +2264 24489 +2277 24709 +2290 24930 +2302 25154 +2315 25379 +2327 25607 +2340 25837 +2352 26069 +2365 26302 +2378 26538 +2390 26776 +2403 27017 +2415 27259 +2428 27504 +2441 27750 +2453 27999 +2466 28250 +2478 28504 +2491 28760 +2503 29018 +2516 29278 +2529 29540 +2541 29805 +2554 30073 +2566 30343 +2579 30615 +2592 30889 +2604 31167 +2617 31446 +2629 31728 +2642 32013 +2655 32300 +2667 32590 +2680 32882 +2692 33177 +2705 33475 +2717 33775 +2730 34078 +2743 34384 +2755 34692 +2768 35003 +2780 35317 +2793 35634 +2806 35954 +2818 36276 +2831 36602 +2843 36930 +2856 37261 +2869 37596 +2881 37933 +2894 38273 +2906 38616 +2919 38963 +2931 39312 +2944 39665 +2957 40021 +2969 40380 +2982 40742 +2994 41108 +3007 41476 +3020 41848 +3032 42224 +3045 42603 +3057 42985 +3070 43370 +3082 43759 +3095 44152 +3108 44548 +3120 44948 +3133 45351 +3145 45758 +3158 46168 +3171 46582 +3183 47000 +3196 47422 +3208 47847 +3221 48276 +3234 48709 +3246 49146 +3259 49587 +4000000 49587 + diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..5dc872fd79c57a0630616d4dc65b24263eb0d126 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 1 (recommended) +The proportion of truncated or collapsed SFS types: 0.015873015873015872 + diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/receipt_51936580.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/receipt_51936580.json new file mode 100644 index 0000000000000000000000000000000000000000..84b6bb92c1c613b70cf41ee5594effb092f4704e --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/receipt_51936580.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "0cd5ed47cdffd61d2a6bfa8e432be480b0a16d9c3f2cc6688f8f820406df68e5", + "elapsed_s": 607, + "failure_sha256": null, + "host": "cn603-26-r", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51936580", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "8549e9c10a5d9fd0a00f6e9355d170826e692726d44e0b109aaf7ac21de09abf", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:15:11Z" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/submissions.jsonl b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..b08564ecfc93efd1a6d804b74dbf05bd09315765 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g0/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g0/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_STEP_DOWN_X10_1K/receipts/export_51933457.json"], "job_id": "51936580", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_STEP_DOWN_X10_1K/fitcoal_g0.json", "request_sha256": "d5e0dbb0acf9a8cafb71b5393823dfaf1ccfd6cfdcb03159bf6d1db05454b46f", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [0], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "8549e9c10a5d9fd0a00f6e9355d170826e692726d44e0b109aaf7ac21de09abf", "stage": "v2", "usage_before": {"account_jobs": 276, "bench_cores": 978, "bench_gpus": 19, "bench_jobs": 206, "bench_pending": 186, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:45:10Z"} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/envlock_check_51938471.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/envlock_check_51938471.json new file mode 100644 index 0000000000000000000000000000000000000000..2a234e55ed0d6dc0d15bb5013bdfb3a807a81dbc --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/envlock_check_51938471.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn603-26-r", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51938471", + "status": "PASS", + "utc": "20260916T120621Z" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fit_spec.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..afe7416fcea4d46023418caa9ae577479976e9b9 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_STEP_DOWN_X10_1K", + "g": 1, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_STEP_DOWN_X10_1K/r00000001/n32" + ], + "rep": 1, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..6957e913dc9a2bfb7dbae91b8e014c40a8edb4a3 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +23235 17688 14128 12957 10994 9702 8504 8336 7958 7119 6715 6127 5601 5326 5032 4621 4508 4182 3879 3718 3699 3349 3271 3108 2983 2776 2912 2594 2603 2382 2391 2203 2210 2182 2133 2022 2142 1832 1772 1867 1895 1707 1777 1666 1738 1618 1705 1510 1574 1611 1543 1318 1365 1372 1394 1352 1252 1224 1324 1375 1225 1304 1237 \ No newline at end of file diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..370deacaf56e23f9d31861d2cbcbaee6d73bad92 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g1/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g1/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 1 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..1b00b2160dfb99ebc12ddcd8b1b41b57f80fbe90 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 35,932 changeTypes: 0 +maxLogL = -20936.499968587013 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 6,189 changeTypes: 1 +standardTime: 0.11039210511870262 generations: 1366.37 N: 50,125 changeTypes: 0 +maxLogL = -442.31538825060215 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 5,803 changeTypes: 2 +standardTime: 0.17776102817249903 generations: 6230.83 N: 99,784 changeTypes: 1 +standardTime: 0.20534269406670544 generations: 11735.27 N: 49,755 changeTypes: 0 +maxLogL = -436.3869448888536 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 6,189 changeTypes: 1 +standardTime: 0.11039210511870262 generations: 1366.37 N: 50,125 changeTypes: 0 +maxLogL = -442.31538825060215 + +computing time = 327.32 seconds diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fitcoal/output.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..3f72a011e67801898c6956f295ac260bb347e188 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 50125 +4000000 50125 + diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/receipt_51938471.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/receipt_51938471.json new file mode 100644 index 0000000000000000000000000000000000000000..17b034ea4aeed18ebfe1102d23e13639dc8f14b9 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/receipt_51938471.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "69578cc2c430d30e93ed2aad0abad3944358d5452371cd1fad346b81f055f2a5", + "elapsed_s": 434, + "failure_sha256": null, + "host": "cn603-26-r", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51938471", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "86267afc8c798cdbb34b20b8afb4155b26847c967064b344bfcadd1b290044e0", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:12:18Z" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/submissions.jsonl b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..c65d8a45097a0c3cfc5cde757333c20bdc2ea9da --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g1/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g1/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_STEP_DOWN_X10_1K/receipts/export_51933457.json"], "job_id": "51938471", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_STEP_DOWN_X10_1K/fitcoal_g1.json", "request_sha256": "83fe8ee56b419d7b377649c7725564687d0482f8c7898030f5428233d6bb8147", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [1], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "86267afc8c798cdbb34b20b8afb4155b26847c967064b344bfcadd1b290044e0", "stage": "v2", "usage_before": {"account_jobs": 278, "bench_cores": 998, "bench_gpus": 20, "bench_jobs": 209, "bench_pending": 187, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:51:24Z"} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/envlock_check_51938935.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/envlock_check_51938935.json new file mode 100644 index 0000000000000000000000000000000000000000..b15cf3c5327c21ccf43a674bed919111b34103be --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/envlock_check_51938935.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn603-26-l", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51938935", + "status": "PASS", + "utc": "20260916T121809Z" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fit_spec.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..8ed29713bcded856937d44ce95e5972552bd2f02 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_STEP_DOWN_X10_1K", + "g": 2, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_STEP_DOWN_X10_1K/r00000002/n32" + ], + "rep": 2, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..e9390fcf11ecc9b432596be07a3ed75dc0cfc670 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +22475 18109 15045 12945 11573 10534 9021 8045 7550 7010 6943 6071 5418 5360 5039 4693 4303 3928 3771 3852 3523 3286 3257 3113 2912 2761 2667 2609 2533 2405 2284 2197 2225 2152 2150 2029 2022 1834 1826 1866 1872 1698 1737 1749 1564 1639 1591 1575 1532 1552 1545 1455 1407 1282 1250 1414 1403 1396 1142 1124 1157 1137 1077 \ No newline at end of file diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..6822d0cf40aceff42b451b21b44e2c7ccb375431 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g2/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g2/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 2 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..728eb83099d693ba0eda7e9399b0f49418eed37d --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 35,902 changeTypes: 0 +maxLogL = -20628.784834279773 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 2,961 changeTypes: 2 +standardTime: 0.1034519406200186 generations: 1831.29 N: 49,124 changeTypes: 0 +maxLogL = -423.6130100585142 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 1,437 changeTypes: 1 +standardTime: 0.0174006762894332 generations: 50.00 N: 7,356 changeTypes: 1 +standardTime: 0.09863877214227536 generations: 1245.10 N: 49,187 changeTypes: 0 +maxLogL = -421.5289846687583 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 2,961 changeTypes: 2 +standardTime: 0.1034519406200186 generations: 1831.29 N: 49,124 changeTypes: 0 +maxLogL = -423.6130100585142 + +computing time = 302.28 seconds diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fitcoal/output.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..f3d74aa20df57a906282756909181b7772cc3b15 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 49124 +4000000 49124 + diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/receipt_51938935.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/receipt_51938935.json new file mode 100644 index 0000000000000000000000000000000000000000..920ea2d1f8223b294563b9ec5f0d70f857c9def4 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/receipt_51938935.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "21a7fe50fee2780d1a1a01337bc382c67a4172708d99d5c7b6f0ab63b30790b9", + "elapsed_s": 1104, + "failure_sha256": null, + "host": "cn603-26-l", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51938935", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "cb84444145398814a55293208db54206afa2944e2635d9785deb2fe0da07fb19", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:23:29Z" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/submissions.jsonl b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..b294ff04de642eecc3c44b8005bcfe62cab2c933 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g2/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g2/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_STEP_DOWN_X10_1K/receipts/export_51933457.json"], "job_id": "51938935", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_STEP_DOWN_X10_1K/fitcoal_g2.json", "request_sha256": "93503b56112ddd74e00839a6a740e59dd941025cf47c666fb98d1f969955d74c", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [2], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "cb84444145398814a55293208db54206afa2944e2635d9785deb2fe0da07fb19", "stage": "v2", "usage_before": {"account_jobs": 278, "bench_cores": 998, "bench_gpus": 20, "bench_jobs": 209, "bench_pending": 188, "never_startable_pending": 0, "throttle_held_not_counted": 0}, "utc": "2026-09-16T11:53:26Z"} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/envlock_check_51940677.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/envlock_check_51940677.json new file mode 100644 index 0000000000000000000000000000000000000000..1c3f1f377cacf6d913556290665420764830542d --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/envlock_check_51940677.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn511-03", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51940677", + "status": "PASS", + "utc": "20260916T122535Z" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fit_spec.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..813c9df2e839fb39c19153f9961744063cfe37ad --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_STEP_DOWN_X10_1K", + "g": 3, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_STEP_DOWN_X10_1K/r00000003/n32" + ], + "rep": 3, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..e4d0a94505891d7326616118f850b02b694a15ec --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +22875 17655 14856 12705 10991 10199 9754 8320 7722 7030 6685 5816 5815 5477 4816 4754 4665 3957 3888 3609 3682 3563 3234 3161 3042 2901 2820 2714 2578 2537 2456 2394 2322 2156 2227 2108 2047 1947 1998 1941 1726 1838 1782 1679 1627 1579 1618 1459 1447 1613 1580 1262 1325 1254 1283 1274 1320 1196 1163 1238 1103 1226 994 \ No newline at end of file diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..6c36d1191390add9fa7771420c3cd5a68d5dd0b4 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g3/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g3/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 2 -randSeed 3 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..3a6c90c8334b4f9150d08a6e8e4a08751cec6668 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 36,026 changeTypes: 0 +maxLogL = -21139.340674665043 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 4,946 changeTypes: 1 +standardTime: 0.10111765923736192 generations: 1000.30 N: 50,021 changeTypes: 0 +maxLogL = -431.9352064892828 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 4,569 changeTypes: 2 +standardTime: 0.13341839797237234 generations: 3258.99 N: 52,432 changeTypes: 1 +standardTime: 1.9989906375194033 generations: 198892.18 N: 40,480 changeTypes: 0 +maxLogL = -411.82590774072105 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 4,946 changeTypes: 1 +standardTime: 0.10111765923736192 generations: 1000.30 N: 50,021 changeTypes: 0 +maxLogL = -431.9352064892828 + +computing time = 192.12 seconds diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fitcoal/output.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..bb5c6e0ef99a322b64958421ee3c2413f4197cf4 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 50021 +4000000 50021 + diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..a58943a48f97b8f2d3333cf34f4a28b685cf1127 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 2 (recommended) +The proportion of truncated or collapsed SFS types: 0.031746031746031744 + diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/receipt_51940677.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/receipt_51940677.json new file mode 100644 index 0000000000000000000000000000000000000000..cd84f44a2327497dfcf7f331e5ae912556b25676 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/receipt_51940677.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "5164b012b900c8a9f3a56cc5058d21fc266ef7d206ed5069f8fd4099a4b257a2", + "elapsed_s": 460, + "failure_sha256": null, + "host": "cn511-03", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51940677", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "d768819bbd93345868ec5dae3a684bb21749be947cf4ddad27751361553e687a", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:28:58Z" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/submissions.jsonl b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..e128f46549db188d840066b425e29cc1ea14b548 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g3/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g3/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_STEP_DOWN_X10_1K/receipts/export_51933457.json"], "job_id": "51940677", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_STEP_DOWN_X10_1K/fitcoal_g3.json", "request_sha256": "a2d39b18600a7a872fe92a9d3f5deeef5dbf5fc2360e416c3ff7cd1b35f0e0c6", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [3], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "d768819bbd93345868ec5dae3a684bb21749be947cf4ddad27751361553e687a", "stage": "v2", "usage_before": {"account_jobs": 171, "bench_cores": 876, "bench_gpus": 4, "bench_jobs": 117, "bench_pending": 22, "never_startable_pending": 0, "throttle_held_not_counted": 5}, "utc": "2026-09-16T12:20:35Z"} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/envlock_check_51940678.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/envlock_check_51940678.json new file mode 100644 index 0000000000000000000000000000000000000000..f9c46ab00bc53a2b92487eb1bf5a004474405146 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/envlock_check_51940678.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn504-17", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51940678", + "status": "PASS", + "utc": "20260916T122537Z" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fit_spec.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..2bebf6df83fcea1403a53d7de619bb85d7742069 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_STEP_DOWN_X10_1K", + "g": 4, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_STEP_DOWN_X10_1K/r00000004/n32" + ], + "rep": 4, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..37771ba456f0d1a608fea61cecd5113c96f8e2a4 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +23011 16990 14923 12944 11582 11087 9312 8860 7437 6769 6259 5939 5593 5482 5007 4469 4320 4038 3936 3935 3578 3373 3189 3057 2892 2875 2811 2530 2400 2550 2492 2332 2467 2261 2118 2098 2115 1860 1853 1845 1837 1687 1804 1683 1704 1545 1550 1491 1546 1501 1454 1563 1302 1232 1282 1374 1223 1424 1151 1286 1199 1047 1103 \ No newline at end of file diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..8925320cb5c8a38471be17ea6943527766863c22 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g4/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g4/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 6 -randSeed 4 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..378ad70447687b2c9179b8ebdb8f0e4b4f3fc492 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 35,770 changeTypes: 0 +maxLogL = -20721.663587754098 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 4,318 changeTypes: 1 +standardTime: 0.09560090284152983 generations: 825.62 N: 49,611 changeTypes: 0 +maxLogL = -429.2292602842417 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 81,323 changeTypes: 2 +standardTime: 0.022791834197180862 generations: 187.20 N: 902 changeTypes: 1 +standardTime: 0.08773878511188113 generations: 304.39 N: 49,467 changeTypes: 0 +maxLogL = -412.5938574649226 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 4,318 changeTypes: 1 +standardTime: 0.09560090284152983 generations: 825.62 N: 49,611 changeTypes: 0 +maxLogL = -429.2292602842417 + +computing time = 160.48 seconds diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fitcoal/output.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..09ed7ca16a3f64dd1aeaea6a5a320c39ca38248a --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 49611 +4000000 49611 + diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..840145fee15c1f0c97f65692dd0d6359c6fcd788 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 6 (recommended) +The proportion of truncated or collapsed SFS types: 0.09523809523809523 + diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/receipt_51940678.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/receipt_51940678.json new file mode 100644 index 0000000000000000000000000000000000000000..ec88ade4df74d9190e0cd87176dfbed02c7582f2 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/receipt_51940678.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "27f5a75f56e31bcbdbbaf7790c82f483028cf68dfe35b118881e7402af116d52", + "elapsed_s": 433, + "failure_sha256": null, + "host": "cn504-17", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51940678", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "1a68af111af9e1ef420c26f5e3ad1250d72eda0ce3143973f23f27d79b678eb2", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:28:31Z" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/submissions.jsonl b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..4ab92b6d1f7ad16fed47b6ce2eb09856715e3e14 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g4/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g4/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_STEP_DOWN_X10_1K/receipts/export_51933457.json"], "job_id": "51940678", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_STEP_DOWN_X10_1K/fitcoal_g4.json", "request_sha256": "0dce462b1b937282c867a3a07bdf3ac5a93a44486cbc5a361e3ed0a3c6cdec46", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [4], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "1a68af111af9e1ef420c26f5e3ad1250d72eda0ce3143973f23f27d79b678eb2", "stage": "v2", "usage_before": {"account_jobs": 172, "bench_cores": 878, "bench_gpus": 4, "bench_jobs": 118, "bench_pending": 23, "never_startable_pending": 0, "throttle_held_not_counted": 5}, "utc": "2026-09-16T12:20:41Z"} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/envlock_check_51940687.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/envlock_check_51940687.json new file mode 100644 index 0000000000000000000000000000000000000000..43ca392b7619231f34c907098e6e803a5bf9e032 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/envlock_check_51940687.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn504-17", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51940687", + "status": "PASS", + "utc": "20260916T122533Z" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fit_spec.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..3d221a4b8c121d266c0f930fe67e92cd98396ad0 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_STEP_DOWN_X10_1K", + "g": 5, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_STEP_DOWN_X10_1K/r00000005/n32" + ], + "rep": 5, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..412e18accdd4fd535963e40d3eaabdd7d3d77d26 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +22838 17393 14580 13127 12337 10558 9111 8140 8156 7285 6412 6337 5651 5152 4784 4491 4553 3982 3909 3629 3637 3529 3296 2992 3106 2866 2925 2664 2480 2568 2377 2379 2244 2072 2166 2036 2043 2036 2039 1992 1818 1839 1712 1640 1765 1736 1574 1493 1525 1390 1491 1389 1375 1335 1405 1360 1307 1285 1328 1298 1190 1150 1107 \ No newline at end of file diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..7957457466b119795e3f717b2b8432e42dddb3b2 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g5/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g5/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 1 -randSeed 5 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..f1a49877f5aa8365847ea7a8d22cc405643c79b6 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 36,256 changeTypes: 0 +maxLogL = -21491.63877159103 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 4,128 changeTypes: 1 +standardTime: 0.09578934694667603 generations: 790.90 N: 50,058 changeTypes: 0 +maxLogL = -434.1542919142812 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 11,250 changeTypes: 1 +standardTime: 0.006681628048675403 generations: 150.34 N: 688 changeTypes: 2 +standardTime: 0.09232465669663226 generations: 662.07 N: 49,940 changeTypes: 0 +maxLogL = -425.96240288825356 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 4,128 changeTypes: 1 +standardTime: 0.09578934694667603 generations: 790.90 N: 50,058 changeTypes: 0 +maxLogL = -434.1542919142812 + +computing time = 170.26 seconds diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fitcoal/output.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..051374a4a2af38536d4e32fd46331e9b1c624cf8 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 50058 +4000000 50058 + diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..5dc872fd79c57a0630616d4dc65b24263eb0d126 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 1 (recommended) +The proportion of truncated or collapsed SFS types: 0.015873015873015872 + diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/receipt_51940687.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/receipt_51940687.json new file mode 100644 index 0000000000000000000000000000000000000000..f7c223ec0b6fe1204b40e3dc3d3b7c45c77b3f3d --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/receipt_51940687.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "94afb154e7dda9e79db2bd04f8379de860011c1dc80ec70d2eee3886b0251ae9", + "elapsed_s": 442, + "failure_sha256": null, + "host": "cn504-17", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51940687", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "877e4279570f6db6660fce0c3cb3b6470b5de4f4b764d1a56d143062e344a4ef", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:28:40Z" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/submissions.jsonl b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..75eaea2879e2a4f55d1009476848fb63ba1b6311 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g5/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g5/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_STEP_DOWN_X10_1K/receipts/export_51933457.json"], "job_id": "51940687", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_STEP_DOWN_X10_1K/fitcoal_g5.json", "request_sha256": "c76c2c7be59a347ab382fa2e983293b03dba5f6bd8827ea5bb9c04fd231408ba", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [5], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "877e4279570f6db6660fce0c3cb3b6470b5de4f4b764d1a56d143062e344a4ef", "stage": "v2", "usage_before": {"account_jobs": 172, "bench_cores": 878, "bench_gpus": 4, "bench_jobs": 118, "bench_pending": 24, "never_startable_pending": 0, "throttle_held_not_counted": 5}, "utc": "2026-09-16T12:20:47Z"} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/envlock_check_51940688.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/envlock_check_51940688.json new file mode 100644 index 0000000000000000000000000000000000000000..4fd9d6646f53e289f8be80071a41145641e63601 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/envlock_check_51940688.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn504-17", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51940688", + "status": "PASS", + "utc": "20260916T122544Z" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fit_spec.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..e577fe40d91a90640a0832f9df6d6b67d8fc564b --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_STEP_DOWN_X10_1K", + "g": 6, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_STEP_DOWN_X10_1K/r00000006/n32" + ], + "rep": 6, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..c4bd20c029b5b2f696bc0247878309f1fa24d4bd --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +22956 17336 14645 12849 11382 10121 8606 8522 7518 7167 6551 6201 5577 5168 4917 4675 4211 4136 4000 3938 3559 3396 3250 3229 3008 2839 2656 2644 2562 2526 2244 2503 2163 2268 2139 2109 2051 1761 1880 1919 1813 1770 1743 1740 1756 1662 1612 1579 1553 1455 1378 1420 1524 1486 1397 1362 1187 1276 1170 1232 1229 1276 1167 \ No newline at end of file diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..a01ba8a6a3afb1ebdd6825fba4bb5e7f736eadf1 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g6/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g6/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 0 -randSeed 6 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..312f4714bbd4d8dacf9aa7ac51f02a3a240f4883 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 35,950 changeTypes: 0 +maxLogL = -21110.87166893428 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 5,369 changeTypes: 1 +standardTime: 0.10455874269284987 generations: 1122.74 N: 49,942 changeTypes: 0 +maxLogL = -406.2813415801893 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 4,644 changeTypes: 2 +standardTime: 0.13416716861754666 generations: 3338.25 N: 53,663 changeTypes: 1 +standardTime: 0.2701408372784321 generations: 17931.80 N: 49,832 changeTypes: 0 +maxLogL = -405.42339793169594 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 5,369 changeTypes: 1 +standardTime: 0.10455874269284987 generations: 1122.74 N: 49,942 changeTypes: 0 +maxLogL = -406.2813415801893 + +computing time = 155.12 seconds diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fitcoal/output.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..bf53a2d514a90d41800903b56e616b6d57c74865 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 49942 +4000000 49942 + diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..44a8b1bae53e9c3cf35c08f98ea3220a1ae26eba --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 0 (recommended) +The proportion of truncated or collapsed SFS types: 0.0 + diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/receipt_51940688.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/receipt_51940688.json new file mode 100644 index 0000000000000000000000000000000000000000..0635bed52c8e1c7f86c64ae28a224c74a40f81fb --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/receipt_51940688.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "f668b17795abd0fd8a7c10361ff63222395c9818e25529b6626e3970281c6f65", + "elapsed_s": 430, + "failure_sha256": null, + "host": "cn504-17", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51940688", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "4ab6609159d26cabee745f77883c830fd51ca5830265f92ae942236a494dbd46", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:28:28Z" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/submissions.jsonl b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..86f9f74cec67ad65382c9b15954e58ef71379f81 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g6/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g6/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_STEP_DOWN_X10_1K/receipts/export_51933457.json"], "job_id": "51940688", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_STEP_DOWN_X10_1K/fitcoal_g6.json", "request_sha256": "49668c56bb7c78a6de23b8d97474718d9126368cb8feaaf8de02d425640a2e06", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [6], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "4ab6609159d26cabee745f77883c830fd51ca5830265f92ae942236a494dbd46", "stage": "v2", "usage_before": {"account_jobs": 173, "bench_cores": 880, "bench_gpus": 4, "bench_jobs": 119, "bench_pending": 25, "never_startable_pending": 0, "throttle_held_not_counted": 5}, "utc": "2026-09-16T12:20:53Z"} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/envlock_check_51940689.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/envlock_check_51940689.json new file mode 100644 index 0000000000000000000000000000000000000000..3dab7f8c5f6c7662c353f0863537d63d8f6cb348 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/envlock_check_51940689.json @@ -0,0 +1,17 @@ +{ + "compared_keys": 165, + "drift": {}, + "host": "cn504-17", + "lock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", + "lock_of_record_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "lock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", + "parts": [ + "envs", + "modules", + "ext" + ], + "schema": "bench_h2h.envlock_gate/1", + "slurm_job_id": "51940689", + "status": "PASS", + "utc": "20260916T122537Z" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fit_spec.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fit_spec.json new file mode 100644 index 0000000000000000000000000000000000000000..6619f73a233a9ac2d6173d66f6d31a332487d468 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fit_spec.json @@ -0,0 +1,24 @@ +{ + "K": 1, + "arm": "EQ", + "config_id": "release_default", + "data_arm": "CLEAN", + "dataset": "v2_a1_STEP_DOWN_X10_1K", + "g": 7, + "method": "fitcoal", + "mu": 1.2500000146076218e-08, + "mu_source": "true", + "n": 32, + "options": {}, + "r": 9.99999993922529e-09, + "regions": [ + "/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_STEP_DOWN_X10_1K/r00000007/n32" + ], + "rep": 7, + "schema": "bench_h2h.fitspec.v1", + "settings": { + "file": "config/tool_settings_v2.json", + "method_call_sha256": "e68a7f904e40c2cf6e2a94be190adc3a9b72639ac15f3b7a3dc441376b37cd71" + }, + "stage": "v2" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fitcoal/afs.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fitcoal/afs.txt new file mode 100644 index 0000000000000000000000000000000000000000..808f7f99d8e9de15528d76bf45444d35f771f872 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fitcoal/afs.txt @@ -0,0 +1 @@ +23126 16737 14268 12252 11135 10098 9000 8303 7103 7028 6396 6137 5348 5346 5046 4685 4465 4044 3646 3830 3376 3351 3422 3185 2876 2921 2710 2655 2616 2515 2697 2345 2458 2133 2268 2086 2076 2055 1899 1942 1834 1765 1609 1887 1548 1574 1605 1449 1574 1534 1583 1394 1448 1330 1237 1312 1255 1390 1231 1316 1294 1238 1249 \ No newline at end of file diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fitcoal/decoder.cmd b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fitcoal/decoder.cmd new file mode 100644 index 0000000000000000000000000000000000000000..b58c3de52006495e60645fc09c5d0e42a2ce6241 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fitcoal/decoder.cmd @@ -0,0 +1 @@ +java -Xmx6g -XX:ParallelGCThreads=2 -XX:CICompilerCount=2 -cp /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/FitCoal.jar FitCoal.calculate.SinglePopDecoder -table /ibex/project/c2041/hany0c/bench_h2h_20260915/ext/fitcoal1.1/tables_n64 -input /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g7/n32/fitcoal/afs.txt -output /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g7/n32/fitcoal/output -generationTime 1 -mutationRate 1.2500000146076218e-05 -omitEndSFS 1 -randSeed 7 -genomeLength 30000.0 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fitcoal/decoder.err b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fitcoal/decoder.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fitcoal/decoder.out b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fitcoal/decoder.out new file mode 100644 index 0000000000000000000000000000000000000000..bd3db17dc74596117269a63059c898fbf47ba109 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fitcoal/decoder.out @@ -0,0 +1,23 @@ +Data:1 +numOfIntervals = 1 +standardTime: 0.0 generations: 0.00 N: 35,649 changeTypes: 0 +maxLogL = -21304.03954625327 + +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 6,358 changeTypes: 1 +standardTime: 0.11572040943553817 generations: 1471.61 N: 50,215 changeTypes: 0 +maxLogL = -439.1843640830666 + +numOfIntervals = 3 +standardTime: 0.0 generations: 0.00 N: 8,565 changeTypes: 1 +standardTime: 0.008860833293847507 generations: 151.79 N: 4,118 changeTypes: 2 +standardTime: 0.1297941112630497 generations: 2865.20 N: 50,222 changeTypes: 0 +maxLogL = -437.74322564603244 + +******** Best: ******** +numOfIntervals = 2 +standardTime: 0.0 generations: 0.00 N: 6,358 changeTypes: 1 +standardTime: 0.11572040943553817 generations: 1471.61 N: 50,215 changeTypes: 0 +maxLogL = -439.1843640830666 + +computing time = 165.26 seconds diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fitcoal/output.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fitcoal/output.txt new file mode 100644 index 0000000000000000000000000000000000000000..bc4b718de5cfbb9ab5054af4689b540758094a9f --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fitcoal/output.txt @@ -0,0 +1,4 @@ +year popSize +2000 50215 +4000000 50215 + diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fitcoal/trunc.err b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fitcoal/trunc.err new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fitcoal/trunc.txt b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fitcoal/trunc.txt new file mode 100644 index 0000000000000000000000000000000000000000..5dc872fd79c57a0630616d4dc65b24263eb0d126 --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/fitcoal/trunc.txt @@ -0,0 +1,7 @@ +Data: 1 +n = 64 +To avoid the effects of positive selection and population structure, the lifted tail of SFS can be removed or collapsed. + +The number of SFS types to be truncated or collapsed: 1 (recommended) +The proportion of truncated or collapsed SFS types: 0.015873015873015872 + diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/receipt_51940689.json b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/receipt_51940689.json new file mode 100644 index 0000000000000000000000000000000000000000..8d44edb79f007b4dce1d782fb9eed3c4731d05be --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/receipt_51940689.json @@ -0,0 +1,18 @@ +{ + "cpus_per_task": "2", + "cuda_visible_devices": null, + "curve_sha256": "83f545483bdfef248da9061d3b68dd1cfa41a835a3af05323f515bb6e918c805", + "elapsed_s": 437, + "failure_sha256": null, + "host": "cn504-17", + "schema": "bench_h2h.tool_receipt.v1", + "script": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", + "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", + "slurm_job_id": "51940689", + "slurm_job_name": "bh2h-fitcoal", + "spec_sha256": "4c51173b2461753b3cf3da8d1ca2b4a35210169af2f4caf7024c62abe3020ec1", + "state": "OK", + "timelimit_s": 28800, + "tool_rc": 0, + "utc": "2026-09-16T12:28:35Z" +} diff --git a/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/submissions.jsonl b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/submissions.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..162a8e1f49056c6d59ecea0a434f9f7b85ba14dc --- /dev/null +++ b/estimates/fitcoal/a1/STEP_DOWN_X10_1K/K1/g7/n32/submissions.jsonl @@ -0,0 +1 @@ +{"argv": ["sbatch", "--parsable", "--cpus-per-task=2", "--mem=16G", "--time=08:00:00", "--export=ALL,BENCH_ENVLOCK=/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/slurm/tool_fitcoal.slurm", "/ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/fitcoal/EQ/release_default/v2_a1_STEP_DOWN_X10_1K/K1/g7/n32/fit_spec.json"], "caps": {"account_jobs": 1900, "cores": 1000, "gpus": 20, "pending": 1500}, "controller_sha256": "3cf3bf07c06b386601d9c513c756b91a8431e0d1633ddb04702b524e0f37b969", "dependency": null, "envlock": "/ibex/project/c2041/hany0c/bench_h2h_20260915/envlock/envlock_20260915T103439Z.json", "envlock_sha256": "2706d39b086f406009c0c09661392edac77d522b5bf2ef8d69b04b468525e1fe", "export_receipts": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/export/v2_a1_STEP_DOWN_X10_1K/receipts/export_51933457.json"], "job_id": "51940689", "mu_provenance": "export meta.json true_mu mean (1 regions)", "request": "/ibex/project/c2041/hany0c/bench_h2h_20260915/v2/driver/requests/v2_a1_STEP_DOWN_X10_1K/fitcoal_g7.json", "request_sha256": "9bcc49f9ca1263dbc69be456984a61d51f607469bd83ac3ad33535d33a699a62", "resources": {"cpus": 2, "gpus": 0, "mem": "16G", "time": "08:00:00"}, "rows": [7], "schema": "bench_h2h.fit_submission.v1", "script_sha256": "87c2d0328db12d226681cafe52b7519111faea239ce6912e8357841e343be0d4", "spec_sha256": "4c51173b2461753b3cf3da8d1ca2b4a35210169af2f4caf7024c62abe3020ec1", "stage": "v2", "usage_before": {"account_jobs": 174, "bench_cores": 882, "bench_gpus": 4, "bench_jobs": 120, "bench_pending": 26, "never_startable_pending": 0, "throttle_held_not_counted": 5}, "utc": "2026-09-16T12:20:59Z"}