Update collection and curation progress 2026-10-14T00:01:49+00:00

README.md

@@ -66,6 +66,6 @@ receive an explicit embedding status; they are never silently cropped.
 
 ## Live progress
 
-Updated 2026-10-13T23:01:48+00:00. Coordinate-qualified candidates before deduplication: **1,454,074**. Final selected unique sequences: **not yet measured**.
+Updated 2026-10-14T00:01:49+00:00. Coordinate-qualified candidates before deduplication: **1,502,672**. 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 2026-10-13T23:01:48+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>1,454,074</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 2026-10-14T00:01:49+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>1,502,672</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 **2026-10-13T23:01:48+00:00**. Target: **1,000,000 distinct sequences with validated structures**.
+Updated **2026-10-14T00:01:49+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) | 1,454,074 |
+| Coordinate-qualified candidates (before global deduplication) | 1,502,672 |
 | Final selected unique sequences | not yet measured |
 | Selected structures uploaded | 0 |
 | Sequences embedded | 60 |
@@ -24,7 +24,7 @@ Source catalog counts are not counts of retrieved or training-ready structures.
 - **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:** complete; coordinate_qualified=1,214,204, validation_rejected=464,863
-- **PDB:** running; entry_processed=86,009, coordinate_qualified=239,870, validation_rejected=7
+- **PDB:** running; entry_processed=103,413, coordinate_qualified=288,468, validation_rejected=11
 - **Final curation:** not started
 - **Upload:** swissprot_candidates_uploaded
 - **ESM-C 6B embeddings:** pilot_complete
@@ -58,15 +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|04:48:31|0:0
-1320625.batch|RUNNING|04:48:31|0:0
-1320625.extern|RUNNING|04:48:31|0:0
+1320625|RUNNING|05:48:32|0:0
+1320625.batch|RUNNING|05:48:32|0:0
+1320625.extern|RUNNING|05:48:32|0:0
 1321100|COMPLETED|00:41:25|0:0
 1321100.batch|COMPLETED|00:41:25|0:0
 1321100.extern|COMPLETED|00:41:25|0:0
 1321145|PENDING|00:00:00|0:0
-1325126|PENDING|00:00:00|0:0
+1326305|PENDING|00:00:00|0:0
 ```
 
-Next hourly update scheduled; remaining updates: 163.
+Next hourly update scheduled; remaining updates: 162.
 </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": "2026-10-13T23:01:48+00:00",
+  "updated_utc": "2026-10-14T00:01:49+00:00",
   "target": 1000000,
   "release_complete": false,
   "inventory": {
@@ -94,12 +94,12 @@
   "pdb": {
     "stage": "running",
     "counts": {
-      "entry_processed": 86009,
-      "coordinate_qualified": 239870,
-      "validation_rejected": 7
+      "entry_processed": 103413,
+      "coordinate_qualified": 288468,
+      "validation_rejected": 11
     },
     "candidate_entry_limit": 163219,
-    "elapsed_seconds": 17307.204545497894
+    "elapsed_seconds": 20892.23717212677
   },
   "primary_sources": [
     "afdb_bulk",
@@ -260,7 +260,7 @@
     "publish_sources": "1320537",
     "afdb_bulk": "1321100",
     "finalize_and_publish": "1321145",
-    "hourly_progress": "1325126"
+    "hourly_progress": "1326305"
   },
   "scheduler": [
     "1320364|COMPLETED|00:01:27|0:0",
@@ -284,26 +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|04:48:31|0:0",
-    "1320625.batch|RUNNING|04:48:31|0:0",
-    "1320625.extern|RUNNING|04:48:31|0:0",
+    "1320625|RUNNING|05:48:32|0:0",
+    "1320625.batch|RUNNING|05:48:32|0:0",
+    "1320625.extern|RUNNING|05:48:32|0:0",
     "1321100|COMPLETED|00:41:25|0:0",
     "1321100.batch|COMPLETED|00:41:25|0:0",
     "1321100.extern|COMPLETED|00:41:25|0:0",
     "1321145|PENDING|00:00:00|0:0",
-    "1325126|PENDING|00:00:00|0:0"
+    "1326305|PENDING|00:00:00|0:0"
   ],
   "next_update": {
     "scheduled": true,
-    "job_id": "1325126",
-    "hourly_updates_remaining": 163
+    "job_id": "1326305",
+    "hourly_updates_remaining": 162
   },
   "queue": [
     {
-      "id": "1325126",
+      "id": "1326305",
       "name": "simplefold-progress",
       "state": "PENDING",
-      "start_cluster_time": "2026-10-13T20:01:48",
+      "start_cluster_time": "2026-10-13T21:01:49",
       "reason": "(BeginTime)"
     },
     {
@@ -324,11 +324,11 @@
   "queue_timezone": "America/New_York",
   "estimates": {
     "pdb": {
-      "candidates_per_second": 4.76017817788526,
-      "remaining_seconds": 16218.510550438667,
-      "planning_low_seconds": 12163.882912829,
-      "planning_high_seconds": 24327.765825658,
-      "finish_utc": "2026-10-14T03:32:06+00:00",
+      "candidates_per_second": 4.855743814072151,
+      "remaining_seconds": 12314.28227879559,
+      "planning_low_seconds": 9235.711709096693,
+      "planning_high_seconds": 18471.423418193386,
+      "finish_utc": "2026-10-14T03:27:03+00:00",
       "basis": "change since previous snapshot",
       "unit": "entries/s",
       "scope": "Completion of candidate attempts, not final eligible unique sequences"
@@ -343,7 +343,7 @@
     {
       "stage": "Progress updates",
       "mode": "Hourly schedule",
-      "detail": "Next job 1325126; 163 scheduled update cycles remain."
+      "detail": "Next job 1326305; 162 scheduled update cycles remain."
     },
     {
       "stage": "Final deduplication and selection",

reports/progress.md

@@ -1,6 +1,6 @@
 # SimpleFoldData — collection and curation progress
 
-Updated **2026-10-13T23:01:48+00:00**. Target: **1,000,000 distinct sequences with validated structures**.
+Updated **2026-10-14T00:01:49+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) | 1,454,074 |
+| Coordinate-qualified candidates (before global deduplication) | 1,502,672 |
 | Final selected unique sequences | not yet measured |
 | Selected structures uploaded | 0 |
 | Sequences embedded | 60 |
@@ -24,7 +24,7 @@ Source catalog counts are not counts of retrieved or training-ready structures.
 - **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:** complete; coordinate_qualified=1,214,204, validation_rejected=464,863
-- **PDB:** running; entry_processed=86,009, coordinate_qualified=239,870, validation_rejected=7
+- **PDB:** running; entry_processed=103,413, coordinate_qualified=288,468, validation_rejected=11
 - **Final curation:** not started
 - **Upload:** swissprot_candidates_uploaded
 - **ESM-C 6B embeddings:** pilot_complete
@@ -58,14 +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|04:48:31|0:0
-1320625.batch|RUNNING|04:48:31|0:0
-1320625.extern|RUNNING|04:48:31|0:0
+1320625|RUNNING|05:48:32|0:0
+1320625.batch|RUNNING|05:48:32|0:0
+1320625.extern|RUNNING|05:48:32|0:0
 1321100|COMPLETED|00:41:25|0:0
 1321100.batch|COMPLETED|00:41:25|0:0
 1321100.extern|COMPLETED|00:41:25|0:0
 1321145|PENDING|00:00:00|0:0
-1325126|PENDING|00:00:00|0:0
+1326305|PENDING|00:00:00|0:0
 ```
 
-Next hourly update scheduled; remaining updates: 163.
+Next hourly update scheduled; remaining updates: 162.