Update collection and curation progress 2026-10-14T04:02:49+00:00

README.md

@@ -66,6 +66,6 @@ receive an explicit embedding status; they are never silently cropped.
 
 ## Live progress
 
-Updated 2026-10-14T03:02:48+00:00. Coordinate-qualified candidates before deduplication: **1,661,108**. Final selected unique sequences: **not yet measured**.
+Updated 2026-10-14T04:02:49+00:00. Coordinate-qualified candidates before deduplication: **1,671,219**. Final selected unique sequences: **1,000,000**.
 
 [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 2026-10-14T03:02:48+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>1,661,108</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 2026-10-14T04:02:49+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>1,671,219</strong></div><div class="card"><span>Final selected unique sequences</span><strong>1,000,000</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 **2026-10-14T03:02:48+00:00**. Target: **1,000,000 distinct sequences with validated structures**.
+Updated **2026-10-14T04:02:49+00:00**. Target: **1,000,000 distinct sequences with validated structures**.
 
 Status: **BUILD IN PROGRESS — final million-chain release not ready**.
 
@@ -10,8 +10,8 @@ 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) | 1,661,108 |
-| Final selected unique sequences | not yet measured |
+| Coordinate-qualified candidates (before global deduplication) | 1,671,219 |
+| Final selected unique sequences | 1,000,000 |
 | Selected structures uploaded | 0 |
 | Sequences embedded | 60 |
 | Embedding bytes stored | 156,194,104 |
@@ -24,8 +24,8 @@ 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=159,467, coordinate_qualified=446,904, validation_rejected=21
-- **Final curation:** not started
+- **PDB:** batch_complete; entry_processed=163,197, coordinate_qualified=457,015, validation_rejected=22
+- **Final curation:** packing_coordinates
 - **Upload:** swissprot_candidates_uploaded
 - **ESM-C 6B embeddings:** pilot_complete
 
@@ -58,15 +58,17 @@ 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|08:49:31|0:0
-1320625.batch|RUNNING|08:49:31|0:0
-1320625.extern|RUNNING|08:49:31|0:0
+1320625|COMPLETED|09:02:24|0:0
+1320625.batch|COMPLETED|09:02:24|0:0
+1320625.extern|COMPLETED|09:02:24|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
-1330077|PENDING|00:00:00|0:0
+1321145|RUNNING|00:47:00|0:0
+1321145.batch|RUNNING|00:47:00|0:0
+1321145.extern|RUNNING|00:47:00|0:0
+1331088|PENDING|00:00:00|0:0
 ```
 
-Next hourly update scheduled; remaining updates: 159.
+Next hourly update scheduled; remaining updates: 158.
 </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": "2026-10-14T03:02:48+00:00",
+  "updated_utc": "2026-10-14T04:02:49+00:00",
   "target": 1000000,
   "release_complete": false,
   "inventory": {
@@ -92,20 +92,29 @@
     "workers": 4
   },
   "pdb": {
-    "stage": "running",
+    "stage": "batch_complete",
     "counts": {
-      "entry_processed": 159467,
-      "coordinate_qualified": 446904,
-      "validation_rejected": 21
+      "entry_processed": 163197,
+      "coordinate_qualified": 457015,
+      "validation_rejected": 22
     },
     "candidate_entry_limit": 163219,
-    "elapsed_seconds": 31752.29718899727
+    "elapsed_seconds": 32543.90879225731
   },
   "primary_sources": [
     "afdb_bulk",
     "pdb"
   ],
-  "curation": {},
+  "curation": {
+    "stage": "packing_coordinates",
+    "updated_unix": 1791950552.930709,
+    "source_records_indexed": 1671219,
+    "selected_unique_sequences": 1000000,
+    "eligible_unique_sequences": 1316099,
+    "target_met": true,
+    "release_complete": false,
+    "coordinate_containers_packed": 1023
+  },
   "upload": {
     "stage": "swissprot_candidates_uploaded",
     "structures_uploaded": 263278,
@@ -260,7 +269,7 @@
     "publish_sources": "1320537",
     "afdb_bulk": "1321100",
     "finalize_and_publish": "1321145",
-    "hourly_progress": "1330077"
+    "hourly_progress": "1331088"
   },
   "scheduler": [
     "1320364|COMPLETED|00:01:27|0:0",
@@ -284,70 +293,54 @@
     "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|08:49:31|0:0",
-    "1320625.batch|RUNNING|08:49:31|0:0",
-    "1320625.extern|RUNNING|08:49:31|0:0",
+    "1320625|COMPLETED|09:02:24|0:0",
+    "1320625.batch|COMPLETED|09:02:24|0:0",
+    "1320625.extern|COMPLETED|09:02:24|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",
-    "1330077|PENDING|00:00:00|0:0"
+    "1321145|RUNNING|00:47:00|0:0",
+    "1321145.batch|RUNNING|00:47:00|0:0",
+    "1321145.extern|RUNNING|00:47:00|0:0",
+    "1331088|PENDING|00:00:00|0:0"
   ],
   "next_update": {
     "scheduled": true,
-    "job_id": "1330077",
-    "hourly_updates_remaining": 159
+    "job_id": "1331088",
+    "hourly_updates_remaining": 158
   },
   "queue": [
     {
-      "id": "1330077",
+      "id": "1331088",
       "name": "simplefold-progress",
       "state": "PENDING",
-      "start_cluster_time": "2026-10-14T00:02:48",
+      "start_cluster_time": "2026-10-14T01:02:49",
       "reason": "(BeginTime)"
     },
     {
       "id": "1321145",
       "name": "simplefold-finalize",
-      "state": "PENDING",
-      "start_cluster_time": "N/A",
-      "reason": "(Dependency)"
-    },
-    {
-      "id": "1320625",
-      "name": "simplefold-pdb",
       "state": "RUNNING",
-      "start_cluster_time": "2026-10-13T14:13:17",
-      "reason": "w0001"
+      "start_cluster_time": "2026-10-13T23:15:49",
+      "reason": "w0002"
     }
   ],
   "queue_timezone": "America/New_York",
-  "estimates": {
-    "pdb": {
-      "candidates_per_second": 5.3143870818065135,
-      "remaining_seconds": 702.0565010728811,
-      "planning_low_seconds": 526.5423758046609,
-      "planning_high_seconds": 1053.0847516093218,
-      "finish_utc": "2026-10-14T03:14:30+00:00",
-      "basis": "change since previous snapshot",
-      "unit": "entries/s",
-      "scope": "Completion of candidate attempts, not final eligible unique sequences"
-    }
-  },
+  "estimates": {},
   "automation": [
     {
       "stage": "AFDB bulk and PDB collection",
-      "mode": "Running",
+      "mode": "See job states",
       "detail": "Pinned AFDB-1.6M coordinate shards replace the API collector. Completed shard validation is checkpointed. PDB collection continues."
     },
     {
       "stage": "Progress updates",
       "mode": "Hourly schedule",
-      "detail": "Next job 1330077; 159 scheduled update cycles remain."
+      "detail": "Next job 1331088; 158 scheduled update cycles remain."
     },
     {
       "stage": "Final deduplication and selection",
-      "mode": "Queued after collection",
+      "mode": "packing_coordinates",
       "detail": "Job 1321145 waits for successful AFDB and PDB jobs. Prefer PDB for exact duplicate sequences; select up to one million."
     },
     {

reports/progress.md

@@ -1,6 +1,6 @@
 # SimpleFoldData — collection and curation progress
 
-Updated **2026-10-14T03:02:48+00:00**. Target: **1,000,000 distinct sequences with validated structures**.
+Updated **2026-10-14T04:02:49+00:00**. Target: **1,000,000 distinct sequences with validated structures**.
 
 Status: **BUILD IN PROGRESS — final million-chain release not ready**.
 
@@ -10,8 +10,8 @@ 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) | 1,661,108 |
-| Final selected unique sequences | not yet measured |
+| Coordinate-qualified candidates (before global deduplication) | 1,671,219 |
+| Final selected unique sequences | 1,000,000 |
 | Selected structures uploaded | 0 |
 | Sequences embedded | 60 |
 | Embedding bytes stored | 156,194,104 |
@@ -24,8 +24,8 @@ 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=159,467, coordinate_qualified=446,904, validation_rejected=21
-- **Final curation:** not started
+- **PDB:** batch_complete; entry_processed=163,197, coordinate_qualified=457,015, validation_rejected=22
+- **Final curation:** packing_coordinates
 - **Upload:** swissprot_candidates_uploaded
 - **ESM-C 6B embeddings:** pilot_complete
 
@@ -58,14 +58,16 @@ 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|08:49:31|0:0
-1320625.batch|RUNNING|08:49:31|0:0
-1320625.extern|RUNNING|08:49:31|0:0
+1320625|COMPLETED|09:02:24|0:0
+1320625.batch|COMPLETED|09:02:24|0:0
+1320625.extern|COMPLETED|09:02:24|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
-1330077|PENDING|00:00:00|0:0
+1321145|RUNNING|00:47:00|0:0
+1321145.batch|RUNNING|00:47:00|0:0
+1321145.extern|RUNNING|00:47:00|0:0
+1331088|PENDING|00:00:00|0:0
 ```
 
-Next hourly update scheduled; remaining updates: 159.
+Next hourly update scheduled; remaining updates: 158.