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encode-chrombpnet-DNASE-ENCSR567EEO-ENCSR855EMN

chrombpnet
encode
chromatin-accessibility
DNASE
spleen
hg38
Model card Files
xet
 Community
chang-m-yun commited on
Commit
d84176e
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1 Parent(s): 31afbdb

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  1. .gitattributes +4 -0
  2. fold_0/logs.models.fold_0.ENCSR567EEO/logfile.modelling.fold_0.ENCSR567EEO.batch_loss.tsv +0 -0
  3. fold_0/logs.models.fold_0.ENCSR567EEO/logfile.modelling.fold_0.ENCSR567EEO.bias_formatting.stderr.txt +38 -0
  4. fold_0/logs.models.fold_0.ENCSR567EEO/logfile.modelling.fold_0.ENCSR567EEO.chrombpnet_formatting.stderr.txt +40 -0
  5. fold_0/logs.models.fold_0.ENCSR567EEO/logfile.modelling.fold_0.ENCSR567EEO.chrombpnet_model_params.tsv +9 -0
  6. fold_0/logs.models.fold_0.ENCSR567EEO/logfile.modelling.fold_0.ENCSR567EEO.chrombpnet_no_bias_formatting.stderr.txt +1 -0
  7. fold_0/logs.models.fold_0.ENCSR567EEO/logfile.modelling.fold_0.ENCSR567EEO.chrombpnet_no_bias_formatting.stdout.txt +1 -0
  8. fold_0/logs.models.fold_0.ENCSR567EEO/logfile.modelling.fold_0.ENCSR567EEO.epoch_loss.csv +19 -0
  9. fold_0/logs.models.fold_0.ENCSR567EEO/logfile.modelling.fold_0.ENCSR567EEO.stdout.txt +3 -0
  10. fold_0/logs.models.fold_0.ENCSR567EEO/logfile.modelling.fold_0.ENCSR567EEO.stdout_v1.txt +3 -0
  11. fold_0/model.bias_scaled.fold_0.ENCSR567EEO.h5 +3 -0
  12. fold_0/model.bias_scaled.fold_0.ENCSR567EEO.tar +3 -0
  13. fold_0/model.chrombpnet.fold_0.ENCSR567EEO.h5 +3 -0
  14. fold_0/model.chrombpnet.fold_0.ENCSR567EEO.tar +3 -0
  15. fold_0/model.chrombpnet_nobias.fold_0.ENCSR567EEO.h5 +3 -0
  16. fold_0/model.chrombpnet_nobias.fold_0.ENCSR567EEO.tar +3 -0
  17. fold_1/model.bias_scaled.fold_1.ENCSR567EEO.h5 +3 -0
  18. fold_1/model.bias_scaled.fold_1.ENCSR567EEO.tar +3 -0
  19. fold_1/model.chrombpnet.fold_1.ENCSR567EEO.h5 +3 -0
  20. fold_1/model.chrombpnet.fold_1.ENCSR567EEO.tar +3 -0
  21. fold_1/model.chrombpnet_nobias.fold_1.ENCSR567EEO.h5 +3 -0
  22. fold_1/model.chrombpnet_nobias.fold_1.ENCSR567EEO.tar +3 -0
  23. fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.args.json +23 -0
  24. fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.batch_loss.tsv +0 -0
  25. fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.bias_formatting.stderr.txt +38 -0
  26. fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.bias_formatting.stdout.txt +1 -0
  27. fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.chrombpnet.params.json +11 -0
  28. fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.chrombpnet_data_params.tsv +3 -0
  29. fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.chrombpnet_formatting.stderr.txt +40 -0
  30. fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.chrombpnet_formatting.stdout.txt +1 -0
  31. fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.chrombpnet_model_params.tsv +9 -0
  32. fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.chrombpnet_no_bias_formatting.stderr.txt +1 -0
  33. fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.chrombpnet_no_bias_formatting.stdout.txt +1 -0
  34. fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.epoch_loss.csv +13 -0
  35. fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.stderr.txt +0 -0
  36. fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.stdout.txt +0 -0
  37. fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.stdout_v1.txt +0 -0
  38. fold_2/model.bias_scaled.fold_2.ENCSR567EEO.h5 +3 -0
  39. fold_2/model.bias_scaled.fold_2.ENCSR567EEO.tar +3 -0
  40. fold_2/model.chrombpnet.fold_2.ENCSR567EEO.h5 +3 -0
  41. fold_2/model.chrombpnet.fold_2.ENCSR567EEO.tar +3 -0
  42. fold_2/model.chrombpnet_nobias.fold_2.ENCSR567EEO.h5 +3 -0
  43. fold_2/model.chrombpnet_nobias.fold_2.ENCSR567EEO.tar +3 -0
  44. fold_3/logs.models.fold_3.ENCSR567EEO/logfile.modelling.fold_3.ENCSR567EEO.stdout.txt +3 -0
  45. fold_3/logs.models.fold_3.ENCSR567EEO/logfile.modelling.fold_3.ENCSR567EEO.stdout_v1.txt +3 -0
  46. fold_3/model.bias_scaled.fold_3.ENCSR567EEO.h5 +3 -0
  47. fold_3/model.bias_scaled.fold_3.ENCSR567EEO.tar +3 -0
  48. fold_3/model.chrombpnet.fold_3.ENCSR567EEO.h5 +3 -0
  49. fold_3/model.chrombpnet.fold_3.ENCSR567EEO.tar +3 -0
  50. fold_3/model.chrombpnet_nobias.fold_3.ENCSR567EEO.h5 +3 -0
.gitattributes CHANGED
@@ -33,3 +33,7 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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  *.zip filter=lfs diff=lfs merge=lfs -text
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  *.zst filter=lfs diff=lfs merge=lfs -text
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  *.zst filter=lfs diff=lfs merge=lfs -text
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  *tfevents* filter=lfs diff=lfs merge=lfs -text
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+ fold_0/logs.models.fold_0.ENCSR567EEO/logfile.modelling.fold_0.ENCSR567EEO.stdout_v1.txt filter=lfs diff=lfs merge=lfs -text
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+ fold_0/logs.models.fold_0.ENCSR567EEO/logfile.modelling.fold_0.ENCSR567EEO.stdout.txt filter=lfs diff=lfs merge=lfs -text
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+ fold_3/logs.models.fold_3.ENCSR567EEO/logfile.modelling.fold_3.ENCSR567EEO.stdout_v1.txt filter=lfs diff=lfs merge=lfs -text
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+ fold_3/logs.models.fold_3.ENCSR567EEO/logfile.modelling.fold_3.ENCSR567EEO.stdout.txt filter=lfs diff=lfs merge=lfs -text
fold_0/logs.models.fold_0.ENCSR567EEO/logfile.modelling.fold_0.ENCSR567EEO.batch_loss.tsv ADDED
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fold_0/logs.models.fold_0.ENCSR567EEO/logfile.modelling.fold_0.ENCSR567EEO.bias_formatting.stderr.txt ADDED
@@ -0,0 +1,38 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 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 02:29:35.966792: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
4
+ 2023-07-15 02:29:38.997799: 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 02:29:39.002050: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
6
+ 2023-07-15 02:29:39.065808: 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
8
+ coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
9
+ 2023-07-15 02:29:39.065873: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
10
+ 2023-07-15 02:29:39.093372: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
11
+ 2023-07-15 02:29:39.093555: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
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+ 2023-07-15 02:29:39.108176: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
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+ 2023-07-15 02:29:39.114411: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
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+ 2023-07-15 02:29:39.136357: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
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+ 2023-07-15 02:29:39.143574: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
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+ 2023-07-15 02:29:39.145219: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
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+ 2023-07-15 02:29:39.147962: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
18
+ 2023-07-15 02:29:39.148337: 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 02:29:39.149311: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
21
+ 2023-07-15 02:29:39.167728: 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
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+ 2023-07-15 02:29:39.167862: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
25
+ 2023-07-15 02:29:39.167927: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
26
+ 2023-07-15 02:29:39.167967: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
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+ 2023-07-15 02:29:39.168000: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
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+ 2023-07-15 02:29:39.168029: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
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+ 2023-07-15 02:29:39.168057: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
30
+ 2023-07-15 02:29:39.168086: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
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+ 2023-07-15 02:29:39.168115: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
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+ 2023-07-15 02:29:39.169158: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
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+ 2023-07-15 02:29:39.170558: 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 02:29:41.024154: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
35
+ 2023-07-15 02:29:41.024250: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267] 0
36
+ 2023-07-15 02:29:41.024287: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0: N
37
+ 2023-07-15 02:29:41.027773: 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 02:29:41.928394: 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.ENCSR567EEO/logfile.modelling.fold_0.ENCSR567EEO.chrombpnet_formatting.stderr.txt ADDED
@@ -0,0 +1,40 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 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 01:26:48.877847: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
4
+ 2023-07-15 01:26:51.339681: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
5
+ 2023-07-15 01:26:51.343665: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
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+ 2023-07-15 01:26:52.807339: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
7
+ pciBusID: 0000:4b:00.0 name: NVIDIA A100-SXM4-80GB computeCapability: 8.0
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+ coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 79.15GiB deviceMemoryBandwidth: 1.85TiB/s
9
+ 2023-07-15 01:26:52.807534: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
10
+ 2023-07-15 01:26:52.831479: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
11
+ 2023-07-15 01:26:52.831530: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
12
+ 2023-07-15 01:26:52.840900: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
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+ 2023-07-15 01:26:52.845428: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
14
+ 2023-07-15 01:26:52.861016: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
15
+ 2023-07-15 01:26:52.865199: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
16
+ 2023-07-15 01:26:52.866105: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
17
+ 2023-07-15 01:26:52.951922: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
18
+ 2023-07-15 01:26:52.952230: 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 01:26:52.953082: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
21
+ 2023-07-15 01:26:53.102824: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
22
+ pciBusID: 0000:4b:00.0 name: NVIDIA A100-SXM4-80GB computeCapability: 8.0
23
+ coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 79.15GiB deviceMemoryBandwidth: 1.85TiB/s
24
+ 2023-07-15 01:26:53.102888: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
25
+ 2023-07-15 01:26:53.102926: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
26
+ 2023-07-15 01:26:53.102952: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
27
+ 2023-07-15 01:26:53.102976: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
28
+ 2023-07-15 01:26:53.102999: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
29
+ 2023-07-15 01:26:53.103021: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
30
+ 2023-07-15 01:26:53.103043: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
31
+ 2023-07-15 01:26:53.103066: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
32
+ 2023-07-15 01:26:53.215028: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
33
+ 2023-07-15 01:26:53.217457: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
34
+ 2023-07-15 01:26:55.010869: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
35
+ 2023-07-15 01:26:55.010953: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267] 0
36
+ 2023-07-15 01:26:55.010965: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0: N
37
+ 2023-07-15 01:26:55.190230: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1406] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 75650 MB memory) -> physical GPU (device: 0, name: NVIDIA A100-SXM4-80GB, pci bus id: 0000:4b:00.0, compute capability: 8.0)
38
+ 2023-07-15 01:26:57.328722: 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.
40
+ , UserWarning)
fold_0/logs.models.fold_0.ENCSR567EEO/logfile.modelling.fold_0.ENCSR567EEO.chrombpnet_model_params.tsv ADDED
@@ -0,0 +1,9 @@
 
 
 
 
 
 
 
 
 
 
1
+ counts_loss_weight 29.2
2
+ filters 512
3
+ n_dil_layers 8
4
+ bias_model_path /scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR567EEO//chrombpnet_model_encsr880cub_bias/bias_model_scaled.h5
5
+ inputlen 2114
6
+ outputlen 1000
7
+ max_jitter 500
8
+ chr_fold_path /scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_0.json
9
+ negative_sampling_ratio 0.1
fold_0/logs.models.fold_0.ENCSR567EEO/logfile.modelling.fold_0.ENCSR567EEO.chrombpnet_no_bias_formatting.stderr.txt ADDED
@@ -0,0 +1 @@
 
 
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//ENCSR567EEO//chrombpnet_model_encsr880cub_bias/chrombpnet_wo_bias.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR567EEO//chrombpnet_model_encsr880cub_bias/new_model_formats/chrombpnet_wo_bias
fold_0/logs.models.fold_0.ENCSR567EEO/logfile.modelling.fold_0.ENCSR567EEO.chrombpnet_no_bias_formatting.stdout.txt ADDED
@@ -0,0 +1 @@
 
 
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//ENCSR567EEO//chrombpnet_model_encsr880cub_bias/chrombpnet_wo_bias.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR567EEO//chrombpnet_model_encsr880cub_bias/new_model_formats/chrombpnet_wo_bias
fold_0/logs.models.fold_0.ENCSR567EEO/logfile.modelling.fold_0.ENCSR567EEO.epoch_loss.csv ADDED
@@ -0,0 +1,19 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ epoch,logcount_predictions_loss,logits_profile_predictions_loss,loss,val_logcount_predictions_loss,val_logits_profile_predictions_loss,val_loss
2
+ 0,1.5955350399017334,990.2730712890625,1036.8631591796875,0.36683449149131775,937.401611328125,948.1133422851562
3
+ 1,0.4118981659412384,948.2074584960938,960.2351684570312,0.3146273195743561,932.3692626953125,941.5563354492188
4
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+ {
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+ "genome": "/scratch/groups/akundaje/anusri/chromatin_atlas/reference/hg38.genome.fa",
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+ "bigwig": "/oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR567EEO//preprocessing/bigWigs/ENCSR567EEO.bigWig",
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+ "trackables": [
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+ "logcount_predictions_loss",
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+ "loss",
11
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+ "seed": 1234,
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23
+ }
fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.batch_loss.tsv ADDED
The diff for this file is too large to render. See raw diff
 
fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.bias_formatting.stderr.txt ADDED
@@ -0,0 +1,38 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 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 02:29:35.998003: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
4
+ 2023-07-15 02:29:38.991453: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
5
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6
+ 2023-07-15 02:29:39.039365: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
7
+ pciBusID: 0000:83:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
8
+ coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
9
+ 2023-07-15 02:29:39.039439: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
10
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11
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12
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13
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14
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15
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17
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18
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19
+ To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
20
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21
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22
+ pciBusID: 0000:83:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
23
+ coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
24
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25
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26
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27
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28
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29
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30
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31
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32
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33
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34
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35
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36
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37
+ 2023-07-15 02:29:41.027813: 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: 0000:83:00.0, compute capability: 6.0)
38
+ 2023-07-15 02:29:41.894648: 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_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.bias_formatting.stdout.txt ADDED
@@ -0,0 +1 @@
 
 
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//ENCSR567EEO//chrombppnet_model_encsr880cub_bias_fold_2/bias_model_scaled.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR567EEO//chrombppnet_model_encsr880cub_bias_fold_2/new_model_formats/bias_model_scaled
fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.chrombpnet.params.json ADDED
@@ -0,0 +1,11 @@
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "counts_loss_weight": "29.0",
3
+ "filters": "512",
4
+ "n_dil_layers": "8",
5
+ "bias_model_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR567EEO//chrombppnet_model_encsr880cub_bias_fold_2/bias_model_scaled.h5",
6
+ "inputlen": "2114",
7
+ "outputlen": "1000",
8
+ "max_jitter": "500",
9
+ "chr_fold_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_2.json",
10
+ "negative_sampling_ratio": "0.1"
11
+ }
fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.chrombpnet_data_params.tsv ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ counts_sum_min_thresh 27.0
2
+ counts_sum_max_thresh 7304.0
3
+ trainings_pts_post_thresh 178182
fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.chrombpnet_formatting.stderr.txt ADDED
@@ -0,0 +1,40 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 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 01:26:48.542531: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
4
+ 2023-07-15 01:26:50.874396: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
5
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6
+ 2023-07-15 01:26:50.995529: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
7
+ pciBusID: 0000:c3:00.0 name: NVIDIA A100-SXM4-80GB computeCapability: 8.0
8
+ coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 79.15GiB deviceMemoryBandwidth: 1.85TiB/s
9
+ 2023-07-15 01:26:50.995611: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
10
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11
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12
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13
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14
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15
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16
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17
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18
+ 2023-07-15 01:26:51.054164: 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 01:26:51.054839: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
21
+ 2023-07-15 01:26:51.057090: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
22
+ pciBusID: 0000:c3:00.0 name: NVIDIA A100-SXM4-80GB computeCapability: 8.0
23
+ coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 79.15GiB deviceMemoryBandwidth: 1.85TiB/s
24
+ 2023-07-15 01:26:51.057116: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
25
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26
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27
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28
+ 2023-07-15 01:26:51.057173: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
29
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30
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33
+ 2023-07-15 01:26:51.062775: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
34
+ 2023-07-15 01:26:54.686457: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
35
+ 2023-07-15 01:26:54.686561: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267] 0
36
+ 2023-07-15 01:26:54.686573: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0: N
37
+ 2023-07-15 01:26:54.693245: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1406] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 75650 MB memory) -> physical GPU (device: 0, name: NVIDIA A100-SXM4-80GB, pci bus id: 0000:c3:00.0, compute capability: 8.0)
38
+ 2023-07-15 01:26:56.723587: 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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fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.chrombpnet_formatting.stdout.txt ADDED
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fold_2/logs.models.fold_2.ENCSR567EEO/logfile.modelling.fold_2.ENCSR567EEO.chrombpnet_model_params.tsv ADDED
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1
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