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encode-chrombpnet-DNASE-posterior-cingulate-gyrus-ENCSR503UFM-ENCSR545CXX

chrombpnet
encode
chromatin-accessibility
DNASE
gyrus
hg38
Model card Files
xet
 Community
chang-m-yun commited on
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1 Parent(s): 1383901

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  1. .gitattributes +10 -0
  2. fold_0/logs.models.fold_0.ENCSR503UFM/logfile.modelling.fold_0.ENCSR503UFM.batch_loss.tsv +0 -0
  3. fold_0/logs.models.fold_0.ENCSR503UFM/logfile.modelling.fold_0.ENCSR503UFM.bias_formatting.stderr.txt +38 -0
  4. fold_0/logs.models.fold_0.ENCSR503UFM/logfile.modelling.fold_0.ENCSR503UFM.chrombpnet.params.json +11 -0
  5. fold_0/logs.models.fold_0.ENCSR503UFM/logfile.modelling.fold_0.ENCSR503UFM.chrombpnet_formatting.stderr.txt +40 -0
  6. fold_0/logs.models.fold_0.ENCSR503UFM/logfile.modelling.fold_0.ENCSR503UFM.chrombpnet_formatting.stdout.txt +1 -0
  7. fold_0/logs.models.fold_0.ENCSR503UFM/logfile.modelling.fold_0.ENCSR503UFM.stdout.txt +3 -0
  8. fold_0/logs.models.fold_0.ENCSR503UFM/logfile.modelling.fold_0.ENCSR503UFM.stdout_v1.txt +3 -0
  9. fold_0/model.bias_scaled.fold_0.ENCSR503UFM.h5 +3 -0
  10. fold_0/model.bias_scaled.fold_0.ENCSR503UFM.tar +3 -0
  11. fold_0/model.chrombpnet.fold_0.ENCSR503UFM.h5 +3 -0
  12. fold_0/model.chrombpnet.fold_0.ENCSR503UFM.tar +3 -0
  13. fold_0/model.chrombpnet_nobias.fold_0.ENCSR503UFM.h5 +3 -0
  14. fold_0/model.chrombpnet_nobias.fold_0.ENCSR503UFM.tar +3 -0
  15. fold_1/logs.models.fold_1.ENCSR503UFM/logfile.modelling.fold_1.ENCSR503UFM.stdout.txt +3 -0
  16. fold_1/logs.models.fold_1.ENCSR503UFM/logfile.modelling.fold_1.ENCSR503UFM.stdout_v1.txt +3 -0
  17. fold_1/model.bias_scaled.fold_1.ENCSR503UFM.h5 +3 -0
  18. fold_1/model.bias_scaled.fold_1.ENCSR503UFM.tar +3 -0
  19. fold_1/model.chrombpnet.fold_1.ENCSR503UFM.h5 +3 -0
  20. fold_1/model.chrombpnet.fold_1.ENCSR503UFM.tar +3 -0
  21. fold_1/model.chrombpnet_nobias.fold_1.ENCSR503UFM.h5 +3 -0
  22. fold_1/model.chrombpnet_nobias.fold_1.ENCSR503UFM.tar +3 -0
  23. fold_2/logs.models.fold_2.ENCSR503UFM/logfile.modelling.fold_2.ENCSR503UFM.args.json +23 -0
  24. fold_2/logs.models.fold_2.ENCSR503UFM/logfile.modelling.fold_2.ENCSR503UFM.batch_loss.tsv +0 -0
  25. fold_2/logs.models.fold_2.ENCSR503UFM/logfile.modelling.fold_2.ENCSR503UFM.bias_formatting.stdout.txt +1 -0
  26. fold_2/logs.models.fold_2.ENCSR503UFM/logfile.modelling.fold_2.ENCSR503UFM.chrombpnet.params.json +11 -0
  27. fold_2/logs.models.fold_2.ENCSR503UFM/logfile.modelling.fold_2.ENCSR503UFM.chrombpnet_data_params.tsv +3 -0
  28. fold_2/logs.models.fold_2.ENCSR503UFM/logfile.modelling.fold_2.ENCSR503UFM.chrombpnet_formatting.stderr.txt +40 -0
  29. fold_2/logs.models.fold_2.ENCSR503UFM/logfile.modelling.fold_2.ENCSR503UFM.chrombpnet_formatting.stdout.txt +1 -0
  30. fold_2/logs.models.fold_2.ENCSR503UFM/logfile.modelling.fold_2.ENCSR503UFM.chrombpnet_model_params.tsv +9 -0
  31. fold_2/logs.models.fold_2.ENCSR503UFM/logfile.modelling.fold_2.ENCSR503UFM.chrombpnet_no_bias_formatting.stderr.txt +1 -0
  32. fold_2/logs.models.fold_2.ENCSR503UFM/logfile.modelling.fold_2.ENCSR503UFM.chrombpnet_no_bias_formatting.stdout.txt +1 -0
  33. fold_2/logs.models.fold_2.ENCSR503UFM/logfile.modelling.fold_2.ENCSR503UFM.epoch_loss.csv +19 -0
  34. fold_2/logs.models.fold_2.ENCSR503UFM/logfile.modelling.fold_2.ENCSR503UFM.stdout.txt +3 -0
  35. fold_2/logs.models.fold_2.ENCSR503UFM/logfile.modelling.fold_2.ENCSR503UFM.stdout_v1.txt +3 -0
  36. fold_2/model.bias_scaled.fold_2.ENCSR503UFM.h5 +3 -0
  37. fold_2/model.bias_scaled.fold_2.ENCSR503UFM.tar +3 -0
  38. fold_2/model.chrombpnet.fold_2.ENCSR503UFM.h5 +3 -0
  39. fold_2/model.chrombpnet.fold_2.ENCSR503UFM.tar +3 -0
  40. fold_2/model.chrombpnet_nobias.fold_2.ENCSR503UFM.h5 +3 -0
  41. fold_2/model.chrombpnet_nobias.fold_2.ENCSR503UFM.tar +3 -0
  42. fold_3/logs.models.fold_3.ENCSR503UFM/logfile.modelling.fold_3.ENCSR503UFM.stdout.txt +3 -0
  43. fold_3/logs.models.fold_3.ENCSR503UFM/logfile.modelling.fold_3.ENCSR503UFM.stdout_v1.txt +3 -0
  44. fold_3/model.bias_scaled.fold_3.ENCSR503UFM.h5 +3 -0
  45. fold_3/model.bias_scaled.fold_3.ENCSR503UFM.tar +3 -0
  46. fold_3/model.chrombpnet.fold_3.ENCSR503UFM.h5 +3 -0
  47. fold_3/model.chrombpnet.fold_3.ENCSR503UFM.tar +3 -0
  48. fold_3/model.chrombpnet_nobias.fold_3.ENCSR503UFM.h5 +3 -0
  49. fold_3/model.chrombpnet_nobias.fold_3.ENCSR503UFM.tar +3 -0
  50. fold_4/logs.models.fold_4.ENCSR503UFM/logfile.modelling.fold_4.ENCSR503UFM.stdout.txt +3 -0
.gitattributes CHANGED
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+ fold_0/logs.models.fold_0.ENCSR503UFM/logfile.modelling.fold_0.ENCSR503UFM.stdout_v1.txt filter=lfs diff=lfs merge=lfs -text
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+ fold_1/logs.models.fold_1.ENCSR503UFM/logfile.modelling.fold_1.ENCSR503UFM.stdout.txt filter=lfs diff=lfs merge=lfs -text
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+ fold_4/logs.models.fold_4.ENCSR503UFM/logfile.modelling.fold_4.ENCSR503UFM.stdout_v1.txt filter=lfs diff=lfs merge=lfs -text
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+ fold_0/logs.models.fold_0.ENCSR503UFM/logfile.modelling.fold_0.ENCSR503UFM.stdout.txt filter=lfs diff=lfs merge=lfs -text
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+ fold_2/logs.models.fold_2.ENCSR503UFM/logfile.modelling.fold_2.ENCSR503UFM.stdout.txt filter=lfs diff=lfs merge=lfs -text
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+ fold_3/logs.models.fold_3.ENCSR503UFM/logfile.modelling.fold_3.ENCSR503UFM.stdout.txt filter=lfs diff=lfs merge=lfs -text
fold_0/logs.models.fold_0.ENCSR503UFM/logfile.modelling.fold_0.ENCSR503UFM.batch_loss.tsv ADDED
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fold_0/logs.models.fold_0.ENCSR503UFM/logfile.modelling.fold_0.ENCSR503UFM.bias_formatting.stderr.txt ADDED
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+ INFO: underlay of /etc/localtime required more than 50 (88) bind mounts
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+ INFO: underlay of /usr/bin/nvidia-smi required more than 50 (355) bind mounts
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+ 2023-07-15 02:50:30.643807: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
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+ 2023-07-15 02:50:33.727150: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
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+ 2023-07-15 02:50:33.732309: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
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+ 2023-07-15 02:50:33.761477: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
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+ pciBusID: 0000:04:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
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+ coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
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+ 2023-07-15 02:50:33.761578: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
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+ 2023-07-15 02:50:33.790561: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
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+ 2023-07-15 02:50:33.790691: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
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+ 2023-07-15 02:50:33.804637: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
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+ 2023-07-15 02:50:33.810867: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
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+ 2023-07-15 02:50:33.833248: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
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+ 2023-07-15 02:50:33.838857: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
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+ 2023-07-15 02:50:33.840020: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
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+ 2023-07-15 02:50:33.841908: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
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+ 2023-07-15 02:50:33.842256: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 FMA
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+ To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
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+ 2023-07-15 02:50:33.843137: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
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+ 2023-07-15 02:50:33.843419: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
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+ pciBusID: 0000:04:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
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+ coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
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+ 2023-07-15 02:50:33.843451: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
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+ 2023-07-15 02:50:33.843476: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
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+ 2023-07-15 02:50:33.843498: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
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+ 2023-07-15 02:50:33.843520: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
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+ 2023-07-15 02:50:33.843541: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
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+ 2023-07-15 02:50:33.843563: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
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+ 2023-07-15 02:50:33.843584: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
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+ 2023-07-15 02:50:33.843605: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
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+ 2023-07-15 02:50:33.843989: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
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+ 2023-07-15 02:50:33.845306: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
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+ 2023-07-15 02:50:35.689538: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
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+ 2023-07-15 02:50:35.689635: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267] 0
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+ 2023-07-15 02:50:35.689656: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0: N
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+ 2023-07-15 02:50:35.692811: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1406] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 14957 MB memory) -> physical GPU (device: 0, name: Tesla P100-PCIE-16GB, pci bus id: 0000:04:00.0, compute capability: 6.0)
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+ 2023-07-15 02:50:36.558365: W tensorflow/python/util/util.cc:348] Sets are not currently considered sequences, but this may change in the future, so consider avoiding using them.
fold_0/logs.models.fold_0.ENCSR503UFM/logfile.modelling.fold_0.ENCSR503UFM.chrombpnet.params.json ADDED
@@ -0,0 +1,11 @@
 
 
 
 
 
 
 
 
 
 
 
 
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+ {
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+ "counts_loss_weight": "14.5",
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+ "filters": "512",
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+ "n_dil_layers": "8",
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+ "bias_model_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR503UFM//chrombpnet_model_encsr880cub_bias/bias_model_scaled.h5",
6
+ "inputlen": "2114",
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+ "outputlen": "1000",
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+ "max_jitter": "500",
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+ "chr_fold_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_0.json",
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+ "negative_sampling_ratio": "0.1"
11
+ }
fold_0/logs.models.fold_0.ENCSR503UFM/logfile.modelling.fold_0.ENCSR503UFM.chrombpnet_formatting.stderr.txt ADDED
@@ -0,0 +1,40 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ INFO: underlay of /etc/localtime required more than 50 (88) bind mounts
2
+ INFO: underlay of /usr/bin/nvidia-smi required more than 50 (355) bind mounts
3
+ 2023-07-15 01:51:51.103187: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
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+ 2023-07-15 01:51:54.193548: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
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+ 2023-07-15 01:51:54.198323: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
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+ 2023-07-15 01:51:54.277438: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
7
+ pciBusID: 0000:82:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
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+ coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
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+ 2023-07-15 01:51:54.277555: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
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+ 2023-07-15 01:51:54.305162: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
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+ 2023-07-15 01:51:54.305295: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
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+ 2023-07-15 01:51:54.318499: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
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+ 2023-07-15 01:51:54.324352: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
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+ 2023-07-15 01:51:54.349627: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
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+ 2023-07-15 01:51:54.355905: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
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+ 2023-07-15 01:51:54.357285: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
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+ 2023-07-15 01:51:54.359295: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
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+ 2023-07-15 01:51:54.359690: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 FMA
19
+ To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
20
+ 2023-07-15 01:51:54.360657: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
21
+ 2023-07-15 01:51:54.360930: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
22
+ pciBusID: 0000:82:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
23
+ coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
24
+ 2023-07-15 01:51:54.360966: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
25
+ 2023-07-15 01:51:54.360996: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
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+ 2023-07-15 01:51:54.361024: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
27
+ 2023-07-15 01:51:54.361052: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
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+ 2023-07-15 01:51:54.361079: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
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+ 2023-07-15 01:51:54.361106: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
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+ 2023-07-15 01:51:54.361133: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
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+ 2023-07-15 01:51:54.361549: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
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+ 2023-07-15 01:51:54.362966: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
34
+ 2023-07-15 01:51:56.192788: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
35
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36
+ 2023-07-15 01:51:56.192925: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0: N
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+ 2023-07-15 01:51:56.195984: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1406] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 14957 MB memory) -> physical GPU (device: 0, name: Tesla P100-PCIE-16GB, pci bus id: 0000:82:00.0, compute capability: 6.0)
38
+ 2023-07-15 01:51:58.691448: W tensorflow/python/util/util.cc:348] Sets are not currently considered sequences, but this may change in the future, so consider avoiding using them.
39
+ /opt/conda/lib/python3.7/site-packages/tensorflow/python/keras/layers/core.py:1059: UserWarning: is not loaded, but a Lambda layer uses it. It may cause errors.
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+ , UserWarning)
fold_0/logs.models.fold_0.ENCSR503UFM/logfile.modelling.fold_0.ENCSR503UFM.chrombpnet_formatting.stdout.txt ADDED
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1
+ singularity exec --nv /home/groups/akundaje/anusri/simg/tf-atlas_gcp-modeling.sif python get_new_tf_model_format.py -i /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR503UFM//chrombpnet_model_encsr880cub_bias/chrombpnet.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR503UFM//chrombpnet_model_encsr880cub_bias/new_model_formats/chrombpnet
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33
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fold_2/logs.models.fold_2.ENCSR503UFM/logfile.modelling.fold_2.ENCSR503UFM.chrombpnet_formatting.stdout.txt ADDED
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fold_2/logs.models.fold_2.ENCSR503UFM/logfile.modelling.fold_2.ENCSR503UFM.chrombpnet_model_params.tsv ADDED
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fold_2/logs.models.fold_2.ENCSR503UFM/logfile.modelling.fold_2.ENCSR503UFM.chrombpnet_no_bias_formatting.stdout.txt ADDED
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fold_2/logs.models.fold_2.ENCSR503UFM/logfile.modelling.fold_2.ENCSR503UFM.epoch_loss.csv ADDED
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