Update collection and curation progress 2026-10-13T18:16:38+00:00

README.md

@@ -60,6 +60,6 @@ receive an explicit embedding status; they are never silently cropped.
 
 ## Live progress
 
-Updated 2026-10-13T18:10:27+00:00. Coordinate-qualified candidates before deduplication: **263,722**. Final selected unique sequences: **not yet measured**.
+Updated 2026-10-13T18:16:38+00:00. Coordinate-qualified candidates before deduplication: **267,477**. 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 2026-10-13T18:10:27+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>263,722</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>0</strong></div><div class="card"><span>Embedding bytes stored</span><strong>0</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 2026-10-13T18:16:38+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
 
-Updated **2026-10-13T18:10:27+00:00**. Target: **1,000,000 distinct sequences with validated structures**.
+Updated **2026-10-13T18:16:38+00:00**. Target: **1,000,000 distinct sequences with validated structures**.
 
 Status: **BUILD IN PROGRESS — final million-chain release not ready**.
 
@@ -10,11 +10,11 @@ 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) | 263,722 |
+| Coordinate-qualified candidates (before global deduplication) | 267,477 |
 | Final selected unique sequences | not yet measured |
 | Structure candidates uploaded | 263,278 |
-| Sequences embedded | 0 |
-| Embedding bytes stored | 0 |
+| Sequences embedded | 60 |
+| Embedding bytes stored | 156,194,104 |
 
 Source catalog counts are not counts of retrieved or training-ready structures. Candidate counts precede global sequence deduplication.
 
@@ -22,11 +22,11 @@ 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=444, source_unavailable=29, confidence_rejected=4
-- **PDB:** not started
+- **AFESM:** running; coordinate_qualified=1,134, source_unavailable=93, confidence_rejected=12
+- **PDB:** running; entry_processed=1,152, coordinate_qualified=3,065
 - **Final curation:** not started
 - **Upload:** swissprot_candidates_uploaded
-- **ESM-C 6B embeddings:** encoder_staged
+- **ESM-C 6B embeddings:** pilot_complete
 
 ## Scope
 
@@ -45,17 +45,22 @@ JobID|State|Elapsed|ExitCode
 1320495|COMPLETED|00:01:05|0:0
 1320495.batch|COMPLETED|00:01:05|0:0
 1320495.extern|COMPLETED|00:01:05|0:0
-1320498|RUNNING|00:00:00|0:0
-1320498.batch|RUNNING|00:00:00|0:0
-1320498.extern|RUNNING|00:00:00|0:0
+1320498|COMPLETED|00:00:42|0:0
+1320498.batch|COMPLETED|00:00:42|0:0
+1320498.extern|COMPLETED|00:00:42|0:0
 1320523|COMPLETED|00:00:43|0:0
 1320523.batch|COMPLETED|00:00:43|0:0
 1320523.extern|COMPLETED|00:00:43|0:0
 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|00:01:37|0:0
-1320554.batch|RUNNING|00:01:37|0:0
-1320554.extern|RUNNING|00:01:37|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
 ```
+
+Next hourly update scheduled; remaining updates: 0.
 </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": "2026-10-13T18:10:27+00:00",
+  "updated_utc": "2026-10-13T18:16:38+00:00",
   "target": 1000000,
   "release_complete": false,
   "inventory": {
@@ -63,17 +63,25 @@
   "afesm": {
     "stage": "running",
     "counts": {
-      "coordinate_qualified": 444,
-      "source_unavailable": 29,
-      "confidence_rejected": 4
+      "coordinate_qualified": 1134,
+      "source_unavailable": 93,
+      "confidence_rejected": 12
     },
-    "attempted": 477,
-    "elapsed_seconds": 85.41513729095459,
-    "processed_this_job": 349,
+    "attempted": 1239,
+    "elapsed_seconds": 456.19149374961853,
+    "processed_this_job": 1111,
     "candidate_limit": 850000,
     "workers": 4
   },
-  "pdb": {},
+  "pdb": {
+    "stage": "running",
+    "counts": {
+      "entry_processed": 1152,
+      "coordinate_qualified": 3065
+    },
+    "candidate_entry_limit": 163219,
+    "elapsed_seconds": 192.826518535614
+  },
   "curation": {},
   "upload": {
     "stage": "swissprot_candidates_uploaded",
@@ -208,14 +216,22 @@
     }
   },
   "embeddings": {
-    "stage": "encoder_staged",
-    "embedded_unique_sequences": 0
+    "stage": "pilot_complete",
+    "embedded_unique_sequences": 60,
+    "pilot_only": true,
+    "total_residues": 30505,
+    "gpu": "NVIDIA B200",
+    "torch": "2.11.0+cu130",
+    "source_unique_sequences_above_2046": 28,
+    "long_sequence_policy": "Retain structures; embeddings beyond 2046 residues need a separately validated policy. No silent cropping.",
+    "bytes": 156194104
   },
   "jobs": {
     "inventory": "1320364",
     "swissprot": "1320405",
     "afesm_pilot": "1320523",
     "afesm_collection": "1320554",
+    "pdb_collection": "1320625",
     "encoder_stage": "1320495",
     "embedding_pilot": "1320498",
     "publish_sources": "1320537"
@@ -230,18 +246,25 @@
     "1320495|COMPLETED|00:01:05|0:0",
     "1320495.batch|COMPLETED|00:01:05|0:0",
     "1320495.extern|COMPLETED|00:01:05|0:0",
-    "1320498|RUNNING|00:00:00|0:0",
-    "1320498.batch|RUNNING|00:00:00|0:0",
-    "1320498.extern|RUNNING|00:00:00|0:0",
+    "1320498|COMPLETED|00:00:42|0:0",
+    "1320498.batch|COMPLETED|00:00:42|0:0",
+    "1320498.extern|COMPLETED|00:00:42|0:0",
     "1320523|COMPLETED|00:00:43|0:0",
     "1320523.batch|COMPLETED|00:00:43|0:0",
     "1320523.extern|COMPLETED|00:00:43|0:0",
     "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|00:01:37|0:0",
-    "1320554.batch|RUNNING|00:01:37|0:0",
-    "1320554.extern|RUNNING|00:01:37|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"
   ],
-  "next_update": {}
+  "next_update": {
+    "scheduled": true,
+    "job_id": "1320419",
+    "hourly_updates_remaining": 168
+  }
 }

reports/progress.md

@@ -1,6 +1,6 @@
 # SimpleFoldData — collection and curation progress
 
-Updated **2026-10-13T18:10:27+00:00**. Target: **1,000,000 distinct sequences with validated structures**.
+Updated **2026-10-13T18:16:38+00:00**. Target: **1,000,000 distinct sequences with validated structures**.
 
 Status: **BUILD IN PROGRESS — final million-chain release not ready**.
 
@@ -10,11 +10,11 @@ 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) | 263,722 |
+| Coordinate-qualified candidates (before global deduplication) | 267,477 |
 | Final selected unique sequences | not yet measured |
 | Structure candidates uploaded | 263,278 |
-| Sequences embedded | 0 |
-| Embedding bytes stored | 0 |
+| Sequences embedded | 60 |
+| Embedding bytes stored | 156,194,104 |
 
 Source catalog counts are not counts of retrieved or training-ready structures. Candidate counts precede global sequence deduplication.
 
@@ -22,11 +22,11 @@ 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=444, source_unavailable=29, confidence_rejected=4
-- **PDB:** not started
+- **AFESM:** running; coordinate_qualified=1,134, source_unavailable=93, confidence_rejected=12
+- **PDB:** running; entry_processed=1,152, coordinate_qualified=3,065
 - **Final curation:** not started
 - **Upload:** swissprot_candidates_uploaded
-- **ESM-C 6B embeddings:** encoder_staged
+- **ESM-C 6B embeddings:** pilot_complete
 
 ## Scope
 
@@ -45,16 +45,21 @@ JobID|State|Elapsed|ExitCode
 1320495|COMPLETED|00:01:05|0:0
 1320495.batch|COMPLETED|00:01:05|0:0
 1320495.extern|COMPLETED|00:01:05|0:0
-1320498|RUNNING|00:00:00|0:0
-1320498.batch|RUNNING|00:00:00|0:0
-1320498.extern|RUNNING|00:00:00|0:0
+1320498|COMPLETED|00:00:42|0:0
+1320498.batch|COMPLETED|00:00:42|0:0
+1320498.extern|COMPLETED|00:00:42|0:0
 1320523|COMPLETED|00:00:43|0:0
 1320523.batch|COMPLETED|00:00:43|0:0
 1320523.extern|COMPLETED|00:00:43|0:0
 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|00:01:37|0:0
-1320554.batch|RUNNING|00:01:37|0:0
-1320554.extern|RUNNING|00:01:37|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
 ```
+
+Next hourly update scheduled; remaining updates: 0.