transfer/code/CCFM/logs/preextract_5402631.out

==========================================
Job ID:    5402631
Job Name:  preextract_scgpt
Start:     Fri Mar 13 23:46:15 JST 2026
Node:      b0034
GPU:       NVIDIA H100, 95830 MiB
==========================================
/home/hp250092/ku50001222/qian/aivc/lfj/transfer/code/scGPT/scgpt/model/model.py:21: UserWarning: flash_attn is not installed
  warnings.warn("flash_attn is not installed")
/home/hp250092/ku50001222/qian/aivc/lfj/transfer/code/scDFM/src/data_process/data.py:185: ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual.
  self.adata.obs['condition'] = self.adata.obs['condition'].str.replace('ctrl', 'control')
/home/hp250092/ku50001222/qian/aivc/lfj/stack_env/lib/python3.13/site-packages/scanpy/preprocessing/_highly_variable_genes.py:806: ImplicitModificationWarning: Trying to modify attribute `._uns` of view, initializing view as actual.
  adata.uns["hvg"] = {"flavor": flavor}
/home/hp250092/ku50001222/qian/aivc/lfj/transfer/code/CCFM/src/data/scgpt_extractor.py:109: UserWarning: FrozenScGPTExtractor: 498/5035 HVG genes not found in scGPT vocab, will use zero vectors.
  warnings.warn(
Device: cuda
Converted var_names to gene symbols, sample: ['RP11-34P13.8', 'RP11-54O7.3', 'SAMD11', 'PERM1', 'HES4']
Warning: ctrl is not in the gene names
Cells: 91205, Genes: 5035
HVG gene names sample: ['RP11-34P13.8', 'RP11-54O7.3', 'SAMD11', 'PERM1', 'HES4']
Valid genes in scGPT vocab: 4537/5035, max_seq_len=4539
Loaded 159/163 pretrained parameters
scGPT d_model: 512
Output: /home/hp250092/ku50001222/qian/aivc/lfj/transfer/code/CCFM/scgpt_cache_norman.h5
Features shape: (91205, 5035, 512) float16

Extracting:   0%|          | 0/357 [00:00<?, ?it/s]/home/hp250092/ku50001222/qian/aivc/lfj/stack_env/lib/python3.13/site-packages/torch/nn/modules/transformer.py:531: UserWarning: The PyTorch API of nested tensors is in prototype stage and will change in the near future. We recommend specifying layout=torch.jagged when constructing a nested tensor, as this layout receives active development, has better operator coverage, and works with torch.compile. (Triggered internally at /pytorch/aten/src/ATen/NestedTensorImpl.cpp:178.)
  output = torch._nested_tensor_from_mask(

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Extracting:  60%|█████▉    | 213/357 [32:33<22:22,  9.32s/it]
Extracting:  60%|█████▉    | 214/357 [32:43<22:16,  9.34s/it]
Extracting:  60%|██████    | 215/357 [32:52<22:08,  9.36s/it]
Extracting:  61%|██████    | 216/357 [33:02<22:00,  9.37s/it]
Extracting:  61%|██████    | 217/357 [33:11<21:53,  9.38s/it]
Extracting:  61%|██████    | 218/357 [33:20<21:44,  9.38s/it]
Extracting:  61%|██████▏   | 219/357 [33:30<21:35,  9.39s/it]
Extracting:  62%|██████▏   | 220/357 [33:39<21:26,  9.39s/it]
Extracting:  62%|██████▏   | 221/357 [33:49<21:17,  9.39s/it]
Extracting:  62%|██████▏   | 222/357 [33:58<21:07,  9.39s/it]
Extracting:  62%|██████▏   | 223/357 [34:07<20:58,  9.39s/it]
Extracting:  63%|██████▎   | 224/357 [34:17<20:48,  9.38s/it]
Extracting:  63%|██████▎   | 225/357 [34:26<20:39,  9.39s/it]
Extracting:  63%|██████▎   | 226/357 [34:36<20:30,  9.39s/it]
Extracting:  64%|██████▎   | 227/357 [34:45<20:21,  9.40s/it]
Extracting:  64%|██████▍   | 228/357 [34:54<20:11,  9.40s/it]
Extracting:  64%|██████▍   | 229/357 [35:04<20:02,  9.39s/it]
Extracting:  64%|██████▍   | 230/357 [35:13<19:53,  9.39s/it]
Extracting:  65%|██████▍   | 231/357 [35:23<19:42,  9.39s/it]
Extracting:  65%|██████▍   | 232/357 [35:32<19:33,  9.39s/it]
Extracting:  65%|██████▌   | 233/357 [35:41<19:23,  9.38s/it]
Extracting:  66%|██████▌   | 234/357 [35:51<19:13,  9.38s/it]
Extracting:  66%|██████▌   | 235/357 [36:00<19:05,  9.39s/it]
Extracting:  66%|██████▌   | 236/357 [36:09<18:55,  9.38s/it]
Extracting:  66%|██████▋   | 237/357 [36:19<18:45,  9.38s/it]
Extracting:  67%|██████▋   | 238/357 [36:28<18:36,  9.38s/it]
Extracting:  67%|██████▋   | 239/357 [36:38<18:26,  9.38s/it]
Extracting:  67%|██████▋   | 240/357 [36:47<18:17,  9.38s/it]
Extracting:  68%|██████▊   | 241/357 [36:56<18:08,  9.39s/it]
Extracting:  68%|██████▊   | 242/357 [37:06<17:58,  9.38s/it]
Extracting:  68%|██████▊   | 243/357 [37:15<17:50,  9.39s/it]
Extracting:  68%|██████▊   | 244/357 [37:25<17:41,  9.40s/it]
Extracting:  69%|██████▊   | 245/357 [37:34<17:32,  9.39s/it]
Extracting:  69%|██████▉   | 246/357 [37:43<17:22,  9.39s/it]
Extracting:  69%|██████▉   | 247/357 [37:53<17:12,  9.39s/it]
Extracting:  69%|██████▉   | 248/357 [38:02<17:03,  9.39s/it]
Extracting:  70%|██████▉   | 249/357 [38:11<16:54,  9.39s/it]
Extracting:  70%|███████   | 250/357 [38:21<16:45,  9.39s/it]
Extracting:  70%|███████   | 251/357 [38:30<16:36,  9.40s/it]
Extracting:  71%|███████   | 252/357 [38:40<16:25,  9.39s/it]
Extracting:  71%|███████   | 253/357 [38:49<16:16,  9.39s/it]
Extracting:  71%|███████   | 254/357 [38:58<16:07,  9.39s/it]
Extracting:  71%|███████▏  | 255/357 [39:08<15:57,  9.39s/it]
Extracting:  72%|███████▏  | 256/357 [39:17<15:48,  9.39s/it]
Extracting:  72%|███████▏  | 257/357 [39:27<15:38,  9.39s/it]
Extracting:  72%|███████▏  | 258/357 [39:36<15:29,  9.39s/it]
Extracting:  73%|███████▎  | 259/357 [39:45<15:19,  9.39s/it]
Extracting:  73%|███████▎  | 260/357 [39:55<15:10,  9.39s/it]
Extracting:  73%|███████▎  | 261/357 [40:04<15:01,  9.39s/it]
Extracting:  73%|███████▎  | 262/357 [40:14<14:52,  9.39s/it]
Extracting:  74%|███████▎  | 263/357 [40:23<14:43,  9.39s/it]
Extracting:  74%|███████▍  | 264/357 [40:32<14:33,  9.39s/it]
Extracting:  74%|███████▍  | 265/357 [40:42<14:24,  9.39s/it]
Extracting:  75%|███████▍  | 266/357 [40:51<14:15,  9.40s/it]
Extracting:  75%|███████▍  | 267/357 [41:01<14:06,  9.40s/it]
Extracting:  75%|███████▌  | 268/357 [41:10<13:56,  9.40s/it]
Extracting:  75%|███████▌  | 269/357 [41:19<13:46,  9.39s/it]
Extracting:  76%|███████▌  | 270/357 [41:29<13:35,  9.38s/it]
Extracting:  76%|███████▌  | 271/357 [41:38<13:26,  9.38s/it]
Extracting:  76%|███████▌  | 272/357 [41:47<13:17,  9.39s/it]
Extracting:  76%|███████▋  | 273/357 [41:57<13:08,  9.39s/it]
Extracting:  77%|███████▋  | 274/357 [42:06<12:59,  9.39s/it]
Extracting:  77%|███████▋  | 275/357 [42:16<12:51,  9.41s/it]
Extracting:  77%|███████▋  | 276/357 [42:25<12:41,  9.41s/it]
Extracting:  78%|███████▊  | 277/357 [42:35<12:32,  9.41s/it]
Extracting:  78%|███████▊  | 278/357 [42:44<12:23,  9.41s/it]
Extracting:  78%|███████▊  | 279/357 [42:53<12:12,  9.40s/it]
Extracting:  78%|███████▊  | 280/357 [43:03<12:04,  9.40s/it]
Extracting:  79%|███████▊  | 281/357 [43:12<11:53,  9.39s/it]
Extracting:  79%|███████▉  | 282/357 [43:21<11:44,  9.39s/it]
Extracting:  79%|███████▉  | 283/357 [43:31<11:34,  9.39s/it]
Extracting:  80%|███████▉  | 284/357 [43:40<11:25,  9.39s/it]
Extracting:  80%|███████▉  | 285/357 [43:50<11:16,  9.39s/it]
Extracting:  80%|████████  | 286/357 [43:59<11:07,  9.40s/it]
Extracting:  80%|████████  | 287/357 [44:08<10:58,  9.40s/it]
Extracting:  81%|████████  | 288/357 [44:18<10:48,  9.40s/it]
Extracting:  81%|████████  | 289/357 [44:27<10:37,  9.38s/it]
Extracting:  81%|████████  | 290/357 [44:37<10:29,  9.39s/it]
Extracting:  82%|████████▏ | 291/357 [44:46<10:19,  9.39s/it]
Extracting:  82%|████████▏ | 292/357 [44:55<10:10,  9.39s/it]
Extracting:  82%|████████▏ | 293/357 [45:05<10:01,  9.39s/it]
Extracting:  82%|████████▏ | 294/357 [45:14<09:50,  9.37s/it]
Extracting:  83%|████████▎ | 295/357 [45:24<09:41,  9.39s/it]
Extracting:  83%|████████▎ | 296/357 [45:33<09:32,  9.39s/it]
Extracting:  83%|████████▎ | 297/357 [45:42<09:23,  9.39s/it]
Extracting:  83%|████████▎ | 298/357 [45:52<09:14,  9.39s/it]
Extracting:  84%|████████▍ | 299/357 [46:01<09:05,  9.40s/it]
Extracting:  84%|████████▍ | 300/357 [46:11<08:55,  9.40s/it]
Extracting:  84%|████████▍ | 301/357 [46:20<08:46,  9.40s/it]
Extracting:  85%|████████▍ | 302/357 [46:29<08:37,  9.40s/it]
Extracting:  85%|████████▍ | 303/357 [46:39<08:27,  9.40s/it]
Extracting:  85%|████████▌ | 304/357 [46:48<08:18,  9.40s/it]
Extracting:  85%|████████▌ | 305/357 [46:58<08:08,  9.40s/it]
Extracting:  86%|████████▌ | 306/357 [47:07<07:59,  9.40s/it]
Extracting:  86%|████████▌ | 307/357 [47:16<07:49,  9.39s/it]
Extracting:  86%|████████▋ | 308/357 [47:26<07:40,  9.40s/it]
Extracting:  87%|████████▋ | 309/357 [47:35<07:30,  9.39s/it]
Extracting:  87%|████████▋ | 310/357 [47:44<07:21,  9.39s/it]
Extracting:  87%|████████▋ | 311/357 [47:54<07:12,  9.40s/it]
Extracting:  87%|████████▋ | 312/357 [48:03<07:02,  9.40s/it]
Extracting:  88%|████████▊ | 313/357 [48:13<06:53,  9.40s/it]
Extracting:  88%|████████▊ | 314/357 [48:22<06:43,  9.39s/it]
Extracting:  88%|████████▊ | 315/357 [48:31<06:34,  9.39s/it]
Extracting:  89%|████████▊ | 316/357 [48:41<06:24,  9.39s/it]
Extracting:  89%|████████▉ | 317/357 [48:50<06:15,  9.40s/it]
Extracting:  89%|████████▉ | 318/357 [49:00<06:06,  9.39s/it]
Extracting:  89%|████████▉ | 319/357 [49:09<05:56,  9.39s/it]
Extracting:  90%|████████▉ | 320/357 [49:18<05:47,  9.39s/it]
Extracting:  90%|████████▉ | 321/357 [49:28<05:38,  9.39s/it]
Extracting:  90%|█████████ | 322/357 [49:37<05:28,  9.39s/it]
Extracting:  90%|█████████ | 323/357 [49:47<05:19,  9.40s/it]
Extracting:  91%|█████████ | 324/357 [49:56<05:09,  9.39s/it]
Extracting:  91%|█████████ | 325/357 [50:05<05:00,  9.39s/it]
Extracting:  91%|█████████▏| 326/357 [50:15<04:51,  9.39s/it]
Extracting:  92%|█████████▏| 327/357 [50:24<04:41,  9.39s/it]
Extracting:  92%|█████████▏| 328/357 [50:34<04:32,  9.39s/it]
Extracting:  92%|█████████▏| 329/357 [50:43<04:22,  9.39s/it]
Extracting:  92%|█████████▏| 330/357 [50:52<04:13,  9.39s/it]
Extracting:  93%|█████████▎| 331/357 [51:02<04:04,  9.39s/it]
Extracting:  93%|█████████▎| 332/357 [51:11<03:54,  9.40s/it]
Extracting:  93%|█████████▎| 333/357 [51:21<03:45,  9.39s/it]
Extracting:  94%|█████████▎| 334/357 [51:30<03:35,  9.38s/it]
Extracting:  94%|█████████▍| 335/357 [51:39<03:26,  9.38s/it]
Extracting:  94%|█████████▍| 336/357 [51:49<03:17,  9.39s/it]
Extracting:  94%|█████████▍| 337/357 [51:58<03:07,  9.40s/it]
Extracting:  95%|█████████▍| 338/357 [52:08<02:58,  9.41s/it]
Extracting:  95%|█████████▍| 339/357 [52:17<02:49,  9.41s/it]
Extracting:  95%|█████████▌| 340/357 [52:26<02:39,  9.41s/it]
Extracting:  96%|█████████▌| 341/357 [52:36<02:30,  9.41s/it]
Extracting:  96%|█████████▌| 342/357 [52:45<02:21,  9.41s/it]
Extracting:  96%|█████████▌| 343/357 [52:55<02:11,  9.40s/it]
Extracting:  96%|█████████▋| 344/357 [53:04<02:02,  9.40s/it]
Extracting:  97%|█████████▋| 345/357 [53:13<01:52,  9.40s/it]
Extracting:  97%|█████████▋| 346/357 [53:23<01:43,  9.39s/it]
Extracting:  97%|█████████▋| 347/357 [53:32<01:33,  9.39s/it]
Extracting:  97%|█████████▋| 348/357 [53:41<01:24,  9.38s/it]
Extracting:  98%|█████████▊| 349/357 [53:51<01:15,  9.38s/it]
Extracting:  98%|█████████▊| 350/357 [54:00<01:05,  9.39s/it]
Extracting:  98%|█████████▊| 351/357 [54:10<00:56,  9.39s/it]
Extracting:  99%|█████████▊| 352/357 [54:19<00:46,  9.39s/it]
Extracting:  99%|█████████▉| 353/357 [54:28<00:37,  9.39s/it]
Extracting:  99%|█████████▉| 354/357 [54:38<00:28,  9.40s/it]
Extracting:  99%|█████████▉| 355/357 [54:47<00:18,  9.39s/it]
Extracting: 100%|█████████▉| 356/357 [54:57<00:09,  9.39s/it]
Extracting: 100%|██████████| 357/357 [55:00<00:00,  7.57s/it]
Extracting: 100%|██████████| 357/357 [55:00<00:00,  9.24s/it]
Global mean range: [-12.3974, 11.9278]
Global var range: [0.0192, 1.8779]
Done! Saved to /home/hp250092/ku50001222/qian/aivc/lfj/transfer/code/CCFM/scgpt_cache_norman.h5
  Features: (91205, 5035, 512) float16
  Valid features counted: 413797085
==========================================
Finished:  Sat Mar 14 00:45:12 JST 2026
==========================================