Update collection and curation progress 2026-10-13T19:00:42+00:00

README.md

@@ -66,6 +66,6 @@ receive an explicit embedding status; they are never silently cropped.
 
 ## Live progress
 
-Updated 2026-10-13T18:44:23+00:00. Coordinate-qualified candidates before deduplication: **157,837**. Final selected unique sequences: **not yet measured**.
+Updated 2026-10-13T19:00:42+00:00. Coordinate-qualified candidates before deduplication: **652,259**. 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 2026-10-13T18:44:23+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>157,837</strong></div><div class="card"><span>Final selected unique sequences</span><strong>not yet measured</strong></div><div class="card"><span>Selected structures uploaded</span><strong>0</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 2026-10-13T19:00:42+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>652,259</strong></div><div class="card"><span>Final selected unique sequences</span><strong>not yet measured</strong></div><div class="card"><span>Selected structures uploaded</span><strong>0</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 **2026-10-13T18:44:23+00:00**. Target: **1,000,000 distinct sequences with validated structures**.
+Updated **2026-10-13T19:00:42+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) | 157,837 |
+| Coordinate-qualified candidates (before global deduplication) | 652,259 |
 | Final selected unique sequences | not yet measured |
 | Selected structures uploaded | 0 |
 | Sequences embedded | 60 |
@@ -23,8 +23,8 @@ 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 (superseded):** superseded; coordinate_qualified=4,477, source_unavailable=403, confidence_rejected=46, validation_rejected=2
-- **AFDB bulk:** running; coordinate_qualified=131,065, validation_rejected=50,375
-- **PDB:** running; entry_processed=9,854, coordinate_qualified=26,772, validation_rejected=2
+- **AFDB bulk:** running; coordinate_qualified=611,811, validation_rejected=234,909
+- **PDB:** running; entry_processed=14,846, coordinate_qualified=40,448, validation_rejected=2
 - **Final curation:** not started
 - **Upload:** swissprot_candidates_uploaded
 - **ESM-C 6B embeddings:** pilot_complete
@@ -43,7 +43,6 @@ 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
@@ -59,14 +58,15 @@ JobID|State|Elapsed|ExitCode
 1320554|CANCELLED by 21014|00:31:03|0:0
 1320554.batch|CANCELLED|00:31:03|0:15
 1320554.extern|COMPLETED|00:31:03|0:0
-1320625|RUNNING|00:31:06|0:0
-1320625.batch|RUNNING|00:31:06|0:0
-1320625.extern|RUNNING|00:31:06|0:0
-1321100|RUNNING|00:04:39|0:0
-1321100.batch|RUNNING|00:04:39|0:0
-1321100.extern|RUNNING|00:04:39|0:0
+1320625|RUNNING|00:47:25|0:0
+1320625.batch|RUNNING|00:47:25|0:0
+1320625.extern|RUNNING|00:47:25|0:0
+1321100|RUNNING|00:20:58|0:0
+1321100.batch|RUNNING|00:20:58|0:0
+1321100.extern|RUNNING|00:20:58|0:0
 1321145|PENDING|00:00:00|0:0
+1321482|PENDING|00:00:00|0:0
 ```
 
-Next hourly update scheduled; remaining updates: 168.
+Next hourly update scheduled; remaining updates: 167.
 </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": "2026-10-13T18:44:23+00:00",
+  "updated_utc": "2026-10-13T19:00:42+00:00",
   "target": 1000000,
   "release_complete": false,
   "inventory": {
@@ -77,16 +77,16 @@
   "afdb_bulk": {
     "stage": "running",
     "counts": {
-      "coordinate_qualified": 131065,
-      "validation_rejected": 50375
+      "coordinate_qualified": 611811,
+      "validation_rejected": 234909
     },
-    "shards_complete": 108,
+    "shards_complete": 504,
     "shards_total": 1000,
-    "rows_processed": 181440,
-    "bytes_complete": 7764109754,
+    "rows_processed": 846720,
+    "bytes_complete": 36162020313,
     "total_bytes": 71689983734,
-    "elapsed_seconds": 276.4593395907432,
-    "shards_this_job": 108,
+    "elapsed_seconds": 1251.9632371477783,
+    "shards_this_job": 504,
     "source_repository": "timodonnell/afdb-1.6M",
     "source_revision": "a7ededeb7caeaef3892f40f2e4df3bb9236b02f8",
     "workers": 4
@@ -94,12 +94,12 @@
   "pdb": {
     "stage": "running",
     "counts": {
-      "entry_processed": 9854,
-      "coordinate_qualified": 26772,
+      "entry_processed": 14846,
+      "coordinate_qualified": 40448,
       "validation_rejected": 2
     },
     "candidate_entry_limit": 163219,
-    "elapsed_seconds": 1859.4233796596527
+    "elapsed_seconds": 2843.4542241096497
   },
   "primary_sources": [
     "afdb_bulk",
@@ -260,7 +260,7 @@
     "publish_sources": "1320537",
     "afdb_bulk": "1321100",
     "finalize_and_publish": "1321145",
-    "hourly_progress": "1320419"
+    "hourly_progress": "1321482"
   },
   "scheduler": [
     "1320364|COMPLETED|00:01:27|0:0",
@@ -269,7 +269,6 @@
     "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",
@@ -285,25 +284,26 @@
     "1320554|CANCELLED by 21014|00:31:03|0:0",
     "1320554.batch|CANCELLED|00:31:03|0:15",
     "1320554.extern|COMPLETED|00:31:03|0:0",
-    "1320625|RUNNING|00:31:06|0:0",
-    "1320625.batch|RUNNING|00:31:06|0:0",
-    "1320625.extern|RUNNING|00:31:06|0:0",
-    "1321100|RUNNING|00:04:39|0:0",
-    "1321100.batch|RUNNING|00:04:39|0:0",
-    "1321100.extern|RUNNING|00:04:39|0:0",
-    "1321145|PENDING|00:00:00|0:0"
+    "1320625|RUNNING|00:47:25|0:0",
+    "1320625.batch|RUNNING|00:47:25|0:0",
+    "1320625.extern|RUNNING|00:47:25|0:0",
+    "1321100|RUNNING|00:20:58|0:0",
+    "1321100.batch|RUNNING|00:20:58|0:0",
+    "1321100.extern|RUNNING|00:20:58|0:0",
+    "1321145|PENDING|00:00:00|0:0",
+    "1321482|PENDING|00:00:00|0:0"
   ],
   "next_update": {
     "scheduled": true,
-    "job_id": "1320419",
-    "hourly_updates_remaining": 168
+    "job_id": "1321482",
+    "hourly_updates_remaining": 167
   },
   "queue": [
     {
-      "id": "1320419",
+      "id": "1321482",
       "name": "simplefold-progress",
       "state": "PENDING",
-      "start_cluster_time": "2026-10-13T15:00:22",
+      "start_cluster_time": "2026-10-13T16:00:42",
       "reason": "(BeginTime)"
     },
     {
@@ -331,21 +331,21 @@
   "queue_timezone": "America/New_York",
   "estimates": {
     "afdb_bulk": {
-      "candidates_per_second": 0.39065419225799314,
-      "remaining_seconds": 2283.3493603235456,
-      "planning_low_seconds": 1712.5120202426592,
-      "planning_high_seconds": 3425.0240404853184,
-      "finish_utc": "2026-10-13T19:22:26+00:00",
+      "candidates_per_second": 0.40594404696045505,
+      "remaining_seconds": 1221.8432656269936,
+      "planning_low_seconds": 916.3824492202452,
+      "planning_high_seconds": 1832.7648984404905,
+      "finish_utc": "2026-10-13T19:21:03+00:00",
       "basis": "change since previous snapshot",
       "unit": "shards/s",
       "scope": "Completion of candidate attempts, not final eligible unique sequences"
     },
     "pdb": {
-      "candidates_per_second": 5.226490729071951,
-      "remaining_seconds": 29343.398457961506,
-      "planning_low_seconds": 22007.54884347113,
-      "planning_high_seconds": 44015.09768694226,
-      "finish_utc": "2026-10-14T02:53:26+00:00",
+      "candidates_per_second": 5.073011713154349,
+      "remaining_seconds": 29247.12348194922,
+      "planning_low_seconds": 21935.342611461914,
+      "planning_high_seconds": 43870.68522292383,
+      "finish_utc": "2026-10-14T03:08:09+00:00",
       "basis": "change since previous snapshot",
       "unit": "entries/s",
       "scope": "Completion of candidate attempts, not final eligible unique sequences"
@@ -360,7 +360,7 @@
     {
       "stage": "Progress updates",
       "mode": "Hourly schedule",
-      "detail": "Next job 1320419; 168 scheduled update cycles remain."
+      "detail": "Next job 1321482; 167 scheduled update cycles remain."
     },
     {
       "stage": "Final deduplication and selection",

reports/progress.md

@@ -1,6 +1,6 @@
 # SimpleFoldData — collection and curation progress
 
-Updated **2026-10-13T18:44:23+00:00**. Target: **1,000,000 distinct sequences with validated structures**.
+Updated **2026-10-13T19:00:42+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) | 157,837 |
+| Coordinate-qualified candidates (before global deduplication) | 652,259 |
 | Final selected unique sequences | not yet measured |
 | Selected structures uploaded | 0 |
 | Sequences embedded | 60 |
@@ -23,8 +23,8 @@ 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 (superseded):** superseded; coordinate_qualified=4,477, source_unavailable=403, confidence_rejected=46, validation_rejected=2
-- **AFDB bulk:** running; coordinate_qualified=131,065, validation_rejected=50,375
-- **PDB:** running; entry_processed=9,854, coordinate_qualified=26,772, validation_rejected=2
+- **AFDB bulk:** running; coordinate_qualified=611,811, validation_rejected=234,909
+- **PDB:** running; entry_processed=14,846, coordinate_qualified=40,448, validation_rejected=2
 - **Final curation:** not started
 - **Upload:** swissprot_candidates_uploaded
 - **ESM-C 6B embeddings:** pilot_complete
@@ -43,7 +43,6 @@ 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
@@ -59,13 +58,14 @@ JobID|State|Elapsed|ExitCode
 1320554|CANCELLED by 21014|00:31:03|0:0
 1320554.batch|CANCELLED|00:31:03|0:15
 1320554.extern|COMPLETED|00:31:03|0:0
-1320625|RUNNING|00:31:06|0:0
-1320625.batch|RUNNING|00:31:06|0:0
-1320625.extern|RUNNING|00:31:06|0:0
-1321100|RUNNING|00:04:39|0:0
-1321100.batch|RUNNING|00:04:39|0:0
-1321100.extern|RUNNING|00:04:39|0:0
+1320625|RUNNING|00:47:25|0:0
+1320625.batch|RUNNING|00:47:25|0:0
+1320625.extern|RUNNING|00:47:25|0:0
+1321100|RUNNING|00:20:58|0:0
+1321100.batch|RUNNING|00:20:58|0:0
+1321100.extern|RUNNING|00:20:58|0:0
 1321145|PENDING|00:00:00|0:0
+1321482|PENDING|00:00:00|0:0
 ```
 
-Next hourly update scheduled; remaining updates: 168.
+Next hourly update scheduled; remaining updates: 167.