Update collection and curation progress 2026-10-13T18:24:47+00:00

README.md

@@ -60,6 +60,6 @@ receive an explicit embedding status; they are never silently cropped.
 
 ## Live progress
 
-Updated 2026-10-13T18:16:38+00:00. Coordinate-qualified candidates before deduplication: **267,477**. Final selected unique sequences: **not yet measured**.
+Updated 2026-10-13T18:24:47+00:00. Coordinate-qualified candidates before deduplication: **275,530**. Final selected unique sequences: **not yet measured**.
 
 [Detailed progress and job status](reports/progress.md) · [Machine-readable status](reports/progress.json) · [HTML dashboard](reports/progress.html)

reports/progress.html

@@ -1,6 +1,6 @@
-<!doctype html><html><head><meta charset="utf-8"><meta name="viewport" content="width=device-width,initial-scale=1"><meta http-equiv="refresh" content="300"><title>SimpleFoldData progress</title><style>body{font:16px system-ui;background:#101922;color:#e6edf3;max-width:1050px;margin:40px auto;padding:24px}h1{font-size:38px}.grid{display:grid;grid-template-columns:repeat(auto-fit,minmax(240px,1fr));gap:14px}.card{background:#1c2b38;border:1px solid #355068;border-radius:12px;padding:20px}.card span{display:block;color:#b7cad8}.card strong{display:block;font-size:30px;margin-top:12px}pre{white-space:pre-wrap;background:#17232e;padding:20px;border-radius:12px}a{color:#8acfff}</style></head><body><h1>SimpleFoldData</h1><p>One million structures · collection and curation</p><p>Updated 2026-10-13T18:16:38+00:00</p><div class="grid"><div class="card"><span>Target distinct sequences</span><strong>1,000,000</strong></div><div class="card"><span>Author AFESM clusters indexed</span><strong>2,036,414</strong></div><div class="card"><span>Author AFESM-E membership rows indexed</span><strong>8,616,595</strong></div><div class="card"><span>Author SwissProt IDs indexed</span><strong>269,003</strong></div><div class="card"><span>Coordinate-qualified candidates (before global deduplication)</span><strong>267,477</strong></div><div class="card"><span>Final selected unique sequences</span><strong>not yet measured</strong></div><div class="card"><span>Structure candidates uploaded</span><strong>263,278</strong></div><div class="card"><span>Sequences embedded</span><strong>60</strong></div><div class="card"><span>Embedding bytes stored</span><strong>156,194,104</strong></div></div><h2>Build details</h2><pre># SimpleFoldData — collection and curation progress
+<!doctype html><html><head><meta charset="utf-8"><meta name="viewport" content="width=device-width,initial-scale=1"><meta http-equiv="refresh" content="300"><title>SimpleFoldData progress</title><style>body{font:16px system-ui;background:#101922;color:#e6edf3;max-width:1050px;margin:40px auto;padding:24px}h1{font-size:38px}.grid{display:grid;grid-template-columns:repeat(auto-fit,minmax(240px,1fr));gap:14px}.card{background:#1c2b38;border:1px solid #355068;border-radius:12px;padding:20px}.card span{display:block;color:#b7cad8}.card strong{display:block;font-size:30px;margin-top:12px}pre{white-space:pre-wrap;background:#17232e;padding:20px;border-radius:12px}a{color:#8acfff}</style></head><body><h1>SimpleFoldData</h1><p>One million structures · collection and curation</p><p>Updated 2026-10-13T18:24:47+00:00</p><div class="grid"><div class="card"><span>Target distinct sequences</span><strong>1,000,000</strong></div><div class="card"><span>Author AFESM clusters indexed</span><strong>2,036,414</strong></div><div class="card"><span>Author AFESM-E membership rows indexed</span><strong>8,616,595</strong></div><div class="card"><span>Author SwissProt IDs indexed</span><strong>269,003</strong></div><div class="card"><span>Coordinate-qualified candidates (before global deduplication)</span><strong>275,530</strong></div><div class="card"><span>Final selected unique sequences</span><strong>not yet measured</strong></div><div class="card"><span>Structure candidates uploaded</span><strong>263,278</strong></div><div class="card"><span>Sequences embedded</span><strong>60</strong></div><div class="card"><span>Embedding bytes stored</span><strong>156,194,104</strong></div></div><h2>Build details</h2><pre># SimpleFoldData — collection and curation progress
 
-Updated **2026-10-13T18:16:38+00:00**. Target: **1,000,000 distinct sequences with validated structures**.
+Updated **2026-10-13T18:24:47+00:00**. Target: **1,000,000 distinct sequences with validated structures**.
 
 Status: **BUILD IN PROGRESS — final million-chain release not ready**.
 
@@ -10,7 +10,7 @@ Status: **BUILD IN PROGRESS — final million-chain release not ready**.
 | Author AFESM clusters indexed | 2,036,414 |
 | Author AFESM-E membership rows indexed | 8,616,595 |
 | Author SwissProt IDs indexed | 269,003 |
-| Coordinate-qualified candidates (before global deduplication) | 267,477 |
+| Coordinate-qualified candidates (before global deduplication) | 275,530 |
 | Final selected unique sequences | not yet measured |
 | Structure candidates uploaded | 263,278 |
 | Sequences embedded | 60 |
@@ -22,8 +22,8 @@ Source catalog counts are not counts of retrieved or training-ready structures.
 
 - **Author inventory:** author_inventory_complete; swissprot_author_rows=269,003, afesm_author_rows=2,036,414, targets=2,305,417, clusters=2,036,414, memberships=8,616,595, afesm_representatives_unmapped=0, members_with_multiple_clusters=0
 - **SwissProt:** complete; coordinate_qualified=263,278, confidence_rejected=5,698, absent_from_available_archive=27
-- **AFESM:** running; coordinate_qualified=1,134, source_unavailable=93, confidence_rejected=12
-- **PDB:** running; entry_processed=1,152, coordinate_qualified=3,065
+- **AFESM:** running; coordinate_qualified=2,262, source_unavailable=205, confidence_rejected=17, validation_rejected=2
+- **PDB:** running; entry_processed=3,710, coordinate_qualified=9,990, validation_rejected=2
 - **Final curation:** not started
 - **Upload:** swissprot_candidates_uploaded
 - **ESM-C 6B embeddings:** pilot_complete
@@ -42,6 +42,7 @@ JobID|State|Elapsed|ExitCode
 1320405|COMPLETED|00:04:15|0:0
 1320405.batch|COMPLETED|00:04:15|0:0
 1320405.extern|COMPLETED|00:04:15|0:0
+1320419|PENDING|00:00:00|0:0
 1320495|COMPLETED|00:01:05|0:0
 1320495.batch|COMPLETED|00:01:05|0:0
 1320495.extern|COMPLETED|00:01:05|0:0
@@ -54,13 +55,13 @@ JobID|State|Elapsed|ExitCode
 1320537|COMPLETED|00:02:11|0:0
 1320537.batch|COMPLETED|00:02:11|0:0
 1320537.extern|COMPLETED|00:02:11|0:0
-1320554|RUNNING|00:07:48|0:0
-1320554.batch|RUNNING|00:07:48|0:0
-1320554.extern|RUNNING|00:07:48|0:0
-1320625|RUNNING|00:03:21|0:0
-1320625.batch|RUNNING|00:03:21|0:0
-1320625.extern|RUNNING|00:03:21|0:0
+1320554|RUNNING|00:15:57|0:0
+1320554.batch|RUNNING|00:15:57|0:0
+1320554.extern|RUNNING|00:15:57|0:0
+1320625|RUNNING|00:11:30|0:0
+1320625.batch|RUNNING|00:11:30|0:0
+1320625.extern|RUNNING|00:11:30|0:0
 ```
 
-Next hourly update scheduled; remaining updates: 0.
+Next hourly update scheduled; remaining updates: 168.
 </pre><p><a href="https://huggingface.co/datasets/kevinlu4588/SimpleFoldData">Public dataset</a></p></body></html>

reports/progress.json

@@ -1,5 +1,5 @@
 {
-  "updated_utc": "2026-10-13T18:16:38+00:00",
+  "updated_utc": "2026-10-13T18:24:47+00:00",
   "target": 1000000,
   "release_complete": false,
   "inventory": {
@@ -63,24 +63,26 @@
   "afesm": {
     "stage": "running",
     "counts": {
-      "coordinate_qualified": 1134,
-      "source_unavailable": 93,
-      "confidence_rejected": 12
+      "coordinate_qualified": 2262,
+      "source_unavailable": 205,
+      "confidence_rejected": 17,
+      "validation_rejected": 2
     },
-    "attempted": 1239,
-    "elapsed_seconds": 456.19149374961853,
-    "processed_this_job": 1111,
+    "attempted": 2486,
+    "elapsed_seconds": 944.421954870224,
+    "processed_this_job": 2358,
     "candidate_limit": 850000,
     "workers": 4
   },
   "pdb": {
     "stage": "running",
     "counts": {
-      "entry_processed": 1152,
-      "coordinate_qualified": 3065
+      "entry_processed": 3710,
+      "coordinate_qualified": 9990,
+      "validation_rejected": 2
     },
     "candidate_entry_limit": 163219,
-    "elapsed_seconds": 192.826518535614
+    "elapsed_seconds": 683.8736047744751
   },
   "curation": {},
   "upload": {
@@ -234,7 +236,8 @@
     "pdb_collection": "1320625",
     "encoder_stage": "1320495",
     "embedding_pilot": "1320498",
-    "publish_sources": "1320537"
+    "publish_sources": "1320537",
+    "hourly_progress": "1320419"
   },
   "scheduler": [
     "1320364|COMPLETED|00:01:27|0:0",
@@ -243,6 +246,7 @@
     "1320405|COMPLETED|00:04:15|0:0",
     "1320405.batch|COMPLETED|00:04:15|0:0",
     "1320405.extern|COMPLETED|00:04:15|0:0",
+    "1320419|PENDING|00:00:00|0:0",
     "1320495|COMPLETED|00:01:05|0:0",
     "1320495.batch|COMPLETED|00:01:05|0:0",
     "1320495.extern|COMPLETED|00:01:05|0:0",
@@ -255,16 +259,88 @@
     "1320537|COMPLETED|00:02:11|0:0",
     "1320537.batch|COMPLETED|00:02:11|0:0",
     "1320537.extern|COMPLETED|00:02:11|0:0",
-    "1320554|RUNNING|00:07:48|0:0",
-    "1320554.batch|RUNNING|00:07:48|0:0",
-    "1320554.extern|RUNNING|00:07:48|0:0",
-    "1320625|RUNNING|00:03:21|0:0",
-    "1320625.batch|RUNNING|00:03:21|0:0",
-    "1320625.extern|RUNNING|00:03:21|0:0"
+    "1320554|RUNNING|00:15:57|0:0",
+    "1320554.batch|RUNNING|00:15:57|0:0",
+    "1320554.extern|RUNNING|00:15:57|0:0",
+    "1320625|RUNNING|00:11:30|0:0",
+    "1320625.batch|RUNNING|00:11:30|0:0",
+    "1320625.extern|RUNNING|00:11:30|0:0"
   ],
   "next_update": {
     "scheduled": true,
     "job_id": "1320419",
     "hourly_updates_remaining": 168
-  }
+  },
+  "queue": [
+    {
+      "id": "1320419",
+      "name": "simplefold-progress",
+      "state": "PENDING",
+      "start_cluster_time": "2026-10-13T15:00:22",
+      "reason": "(BeginTime)"
+    },
+    {
+      "id": "1320625",
+      "name": "simplefold-pdb",
+      "state": "RUNNING",
+      "start_cluster_time": "2026-10-13T14:13:17",
+      "reason": "w0001"
+    },
+    {
+      "id": "1320554",
+      "name": "simplefold-afesm",
+      "state": "RUNNING",
+      "start_cluster_time": "2026-10-13T14:08:50",
+      "reason": "w0004"
+    }
+  ],
+  "queue_timezone": "America/New_York",
+  "estimates": {
+    "afesm": {
+      "candidates_per_second": 2.5541216685616814,
+      "remaining_seconds": 331822.09384616587,
+      "planning_low_seconds": 248866.5703846244,
+      "planning_high_seconds": 497733.1407692488,
+      "finish_utc": "2026-10-17T14:35:09+00:00",
+      "basis": "change since previous snapshot",
+      "scope": "Completion of candidate attempts, not final eligible unique sequences"
+    },
+    "pdb": {
+      "candidates_per_second": 5.213349333987767,
+      "remaining_seconds": 30595.877962774222,
+      "planning_low_seconds": 22946.908472080668,
+      "planning_high_seconds": 45893.816944161335,
+      "finish_utc": "2026-10-14T02:54:42+00:00",
+      "basis": "change since previous snapshot",
+      "scope": "Completion of candidate attempts, not final eligible unique sequences"
+    }
+  },
+  "automation": [
+    {
+      "stage": "AFESM and PDB collection",
+      "mode": "Automatic continuation",
+      "detail": "Collectors submit a successor at their 18-hour checkpoint until their configured candidate limits. Failures require attention."
+    },
+    {
+      "stage": "Progress updates",
+      "mode": "Hourly schedule",
+      "detail": "Next job 1320419; 168 scheduled update cycles remain."
+    },
+    {
+      "stage": "Final deduplication and selection",
+      "mode": "Not queued",
+      "detail": "Requires completed source pool and a final selection job."
+    },
+    {
+      "stage": "ESM-C 6B production embeddings",
+      "mode": "Not queued",
+      "detail": "60-sequence pilot complete; full cache production has not been launched."
+    },
+    {
+      "stage": "Remaining uploads and final release",
+      "mode": "Not queued",
+      "detail": "SwissProt candidates are uploaded. AFESM/PDB shards and final release still need publishing jobs."
+    }
+  ],
+  "eta_note": "Throughput projections for candidate collection only. Planning ranges are 0.75\u20131.5 times the projection, not confidence intervals. Excludes future queue delays, outages, final curation, production embeddings and uploads. End-to-end completion is not yet estimated."
 }

reports/progress.md

@@ -1,6 +1,6 @@
 # SimpleFoldData — collection and curation progress
 
-Updated **2026-10-13T18:16:38+00:00**. Target: **1,000,000 distinct sequences with validated structures**.
+Updated **2026-10-13T18:24:47+00:00**. Target: **1,000,000 distinct sequences with validated structures**.
 
 Status: **BUILD IN PROGRESS — final million-chain release not ready**.
 
@@ -10,7 +10,7 @@ Status: **BUILD IN PROGRESS — final million-chain release not ready**.
 | Author AFESM clusters indexed | 2,036,414 |
 | Author AFESM-E membership rows indexed | 8,616,595 |
 | Author SwissProt IDs indexed | 269,003 |
-| Coordinate-qualified candidates (before global deduplication) | 267,477 |
+| Coordinate-qualified candidates (before global deduplication) | 275,530 |
 | Final selected unique sequences | not yet measured |
 | Structure candidates uploaded | 263,278 |
 | Sequences embedded | 60 |
@@ -22,8 +22,8 @@ Source catalog counts are not counts of retrieved or training-ready structures.
 
 - **Author inventory:** author_inventory_complete; swissprot_author_rows=269,003, afesm_author_rows=2,036,414, targets=2,305,417, clusters=2,036,414, memberships=8,616,595, afesm_representatives_unmapped=0, members_with_multiple_clusters=0
 - **SwissProt:** complete; coordinate_qualified=263,278, confidence_rejected=5,698, absent_from_available_archive=27
-- **AFESM:** running; coordinate_qualified=1,134, source_unavailable=93, confidence_rejected=12
-- **PDB:** running; entry_processed=1,152, coordinate_qualified=3,065
+- **AFESM:** running; coordinate_qualified=2,262, source_unavailable=205, confidence_rejected=17, validation_rejected=2
+- **PDB:** running; entry_processed=3,710, coordinate_qualified=9,990, validation_rejected=2
 - **Final curation:** not started
 - **Upload:** swissprot_candidates_uploaded
 - **ESM-C 6B embeddings:** pilot_complete
@@ -42,6 +42,7 @@ JobID|State|Elapsed|ExitCode
 1320405|COMPLETED|00:04:15|0:0
 1320405.batch|COMPLETED|00:04:15|0:0
 1320405.extern|COMPLETED|00:04:15|0:0
+1320419|PENDING|00:00:00|0:0
 1320495|COMPLETED|00:01:05|0:0
 1320495.batch|COMPLETED|00:01:05|0:0
 1320495.extern|COMPLETED|00:01:05|0:0
@@ -54,12 +55,12 @@ JobID|State|Elapsed|ExitCode
 1320537|COMPLETED|00:02:11|0:0
 1320537.batch|COMPLETED|00:02:11|0:0
 1320537.extern|COMPLETED|00:02:11|0:0
-1320554|RUNNING|00:07:48|0:0
-1320554.batch|RUNNING|00:07:48|0:0
-1320554.extern|RUNNING|00:07:48|0:0
-1320625|RUNNING|00:03:21|0:0
-1320625.batch|RUNNING|00:03:21|0:0
-1320625.extern|RUNNING|00:03:21|0:0
+1320554|RUNNING|00:15:57|0:0
+1320554.batch|RUNNING|00:15:57|0:0
+1320554.extern|RUNNING|00:15:57|0:0
+1320625|RUNNING|00:11:30|0:0
+1320625.batch|RUNNING|00:11:30|0:0
+1320625.extern|RUNNING|00:11:30|0:0
 ```
 
-Next hourly update scheduled; remaining updates: 0.
+Next hourly update scheduled; remaining updates: 168.