Add ph/d/biological/udance/logs/h100-run-20260813/

ph/d/biological/udance/logs/h100-run-20260813/README.md

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+# uDance 200K gene-tree run logs (H100 hpegpu-server, 2026-08-13/14)
+
+Recovered 2026-11-01 from hpegpu-server:/data/phylogeny/data/outputs (run as gpuadmin, read as user4).
+Pipeline: udance-data-processing (scripts/run_gene_trees.py), FastTreeMP 2.2.0 `-lg -gamma`, 2 OpenMP threads per gene.
+Final concatenated gene trees: ../../gt/udance-gt-200k-fasttreemp__model_lg__gamma.tre (3.9 GB).
+
+Files
+- manifest.tsv: one row per gene: source, taxa, sites, status, seconds, command (380 genes, all success).
+- run_ranges.tsv: the single invocation, start/finish UTC, host.
+- udance-h100-logs-20260813.tar.gz (35 MB): everything under outputs/ except trees:
+  - udance-data-processing/full/200k-fasttreemp__model_lg__gamma/: logs/p*.log (380 per-gene FastTree logs, start time, elapsed, exit code), manifest, run_ranges, ntfy-outbox (376 unsent progress messages), hf-upload-outbox/receipts (most per-gene HF uploads never went through, so only 4 logs were mirrored under on-progress/).
+  - udance-data-processing/full/16k-fasttreemp__model_lg__gamma/: 84 logs of an early partial 16K run (the complete 16K set is ../../processed/16k-...zip).
+  - astralx/udance/: ASTRAL-X logs/stats/scores on 16K and 200K (incl. the 200K ref-st scoring and the S1-I3 crash).
+- Not recoverable without the gpuadmin account (mode 600 / private home): summary.json, run_config.json, gene_trees_present.txt, Slurm/terminal output and crash reports in /home/gpuadmin.
+
+Run requirements (200K, measured)
+- Wall time: 19.2 h (2026-08-13 11:31 -> 2026-08-14 06:41 UTC), one invocation, 0 failures.
+- Compute: 589 gene-hours in total (each gene: 2 threads); per gene median 88 min, min 33 min, max 3.8 h; ~31 genes ran at once on average (~62 of 64 cores).
+- Genes: 380; 110k-652k taxa per gene (median 612k), 1344-2257 sites.
+- Disk: input archives 200K-ALNS-1/2.tar 3.3 GB; decompressed alignment cache 351 GB (the big one); per-gene trees 3.7 GB + concatenated 3.9 GB; logs 272 MB. Total /data/phylogeny today 383 GB.
+- RAM: not logged by the pipeline.

ph/d/biological/udance/logs/h100-run-20260813/run_ranges.tsv

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+started_utc	finished_utc	hostname	start_gene	end_gene	selected_genes	successful_or_resumed	failed	dry_run
+2026-08-13T11:31:02.649640+00:00	2026-08-14T06:41:13.224113+00:00	hpegpu-server	first	last	380	380	0	False

ph/d/biological/udance/logs/h100-run-20260813/udance-h100-logs-20260813.tar.gz

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