Upload folder using huggingface_hub

.gitattributes

@@ -33,3 +33,12 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+fold_0/logs.models.fold_0.ENCSR866ODX/logfile.modelling.fold_0.ENCSR866ODX.stdout_v1.txt filter=lfs diff=lfs merge=lfs -text
+fold_1/logs.models.fold_1.ENCSR866ODX/logfile.modelling.fold_1.ENCSR866ODX.stdout.txt filter=lfs diff=lfs merge=lfs -text
+fold_1/logs.models.fold_1.ENCSR866ODX/logfile.modelling.fold_1.ENCSR866ODX.stdout_v1.txt filter=lfs diff=lfs merge=lfs -text
+fold_2/logs.models.fold_2.ENCSR866ODX/logfile.modelling.fold_2.ENCSR866ODX.stdout.txt filter=lfs diff=lfs merge=lfs -text
+fold_2/logs.models.fold_2.ENCSR866ODX/logfile.modelling.fold_2.ENCSR866ODX.stdout_v1.txt filter=lfs diff=lfs merge=lfs -text
+fold_3/logs.models.fold_3.ENCSR866ODX/logfile.modelling.fold_3.ENCSR866ODX.stdout.txt filter=lfs diff=lfs merge=lfs -text
+fold_3/logs.models.fold_3.ENCSR866ODX/logfile.modelling.fold_3.ENCSR866ODX.stdout_v1.txt filter=lfs diff=lfs merge=lfs -text
+fold_4/logs.models.fold_4.ENCSR866ODX/logfile.modelling.fold_4.ENCSR866ODX.stdout.txt filter=lfs diff=lfs merge=lfs -text
+fold_4/logs.models.fold_4.ENCSR866ODX/logfile.modelling.fold_4.ENCSR866ODX.stdout_v1.txt filter=lfs diff=lfs merge=lfs -text

README.md

@@ -0,0 +1,120 @@
+---
+license: mit
+library_name: chrombpnet
+tags:
+  - encode
+  - chrombpnet
+  - chromatin-accessibility
+  - DNASE
+  - testis
+  - hg38
+---
+# ENCODE ChromBPNet Atlas
+As part of the ENCODE 4 Project, we trained ChromBPNet models on 1,512 ENCODE DNAse-seq and ATAC-seq across 408 biosamples. Here, we provide all models for open-source use.
+
+For more information about the models, see:
+- Main ENCODE 4 Paper
+- [A unified lexicon of predictive DNA sequence motifs from ENCODE transcription factor binding and chromatin accessibility assays](https://doi.org/10.5281/zenodo.17123347) (Deshpande et al., Zenodo 2025)
+- [ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants](https://doi.org/10.1101/2024.12.25.630221) (Pampari et al., bioRxiv 2024)
+
+## ChromBPNet model: DNASE in testis (ENCSR866ODX)
+- Model: ChromBPNet
+- Assay: DNASE-seq
+- Experiment: [ENCSR866ODX](https://www.encodeproject.org/experiments/ENCSR866ODX/)
+- Model annotation: [ENCSR782JTX](https://www.encodeproject.org/annotations/ENCSR782JTX/)
+- Biosample: testis (Full name: Homo sapiens testis tissue male adult (37 years))
+- Cell slim(s): None
+- Organ slim(s): testis,gonad
+- Developmental slim(s): None
+- System slim(s): reproductive-system
+- Assembly: hg38
+
+## Directory structure
+- `fold_0`: Model of 5-fold cross-validation: Fold 0
+    - `model.chrombpnet.fold_0.encid.h5`: full chrombpnet model that combines both bias and corrected model in .h5 format
+    - `model.chrombpnet_nobias.fold_0.encid.h5`: bias-corrected accessibility model in .h5 format (Use for all biological discovery)
+    - `model.bias_scaled.fold_0.encid.h5`: bias model in .h5 format
+    - `model.chrombpnet.fold_0.encid.tar`: full chrombpnet model that combines both bias and  corrected model in SavedModel format. After being untarred, it results in a directory named "chrombpnet".
+    - `model.chrombpnet_nobias.fold_0.encid.tar`: bias-corrected accessibility model in SavedModel format (Use for all biological discovery). After being untarred, it results in a directory named "chrombpnet_wo_bias".
+    - `model.bias_scaled.fold_0.encid.tar`: bias model in SavedModel format. After being untarred, it results in a directory named "bias_model_scaled".
+    - `logs.models.fold_0.encid`: folder containing log files for training models
+- `fold_1`: Model of 5-fold coss-validation: Fold 1
+- `fold_2`: Model of 5-fold cross-validation: Fold 2
+- `fold_3`: Model of 5-fold cross-validation: Fold 3
+- `fold_4`: Model of 5-fold cross-validation: Fold 4
+
+# Instructions
+## 1. Pseudocode for loading models in .h5 format 
+
+(1) Use the code in python after appropriately defining `model_in_h5_format` and `inputs`. \
+(2) `inputs` is a one hot encoded sequence of shape (N,2114,4). Here N corresponds to the 
+number of tested sequences, 2114 is the input sequence length and 4 corresponds to [A,C,G,T].
+
+```python
+import tensorflow as tf
+from tensorflow.keras.utils import get_custom_objects
+from tensorflow.keras.models import load_model
+
+custom_objects={"tf": tf}
+get_custom_objects().update(custom_objects)
+
+model=load_model(model_in_h5_format,compile=False)
+outputs = model(inputs)
+```
+
+The list `outputs` consists of two elements. The first element has a shape of (N, 1000) and
+contains logit predictions for a 1000-base-pair output. The second element, with a shape of
+(N, 1), contains logcount predictions. To transform these predictions into per-base signals, 
+follow the provided pseudo code lines below.
+
+```python
+import numpy as np
+
+def softmax(x, temp=1):
+    norm_x = x - np.mean(x,axis=1, keepdims=True)
+    return np.exp(temp*norm_x)/np.sum(np.exp(temp*norm_x), axis=1, keepdims=True)
+    
+predictions = softmax(outputs[0]) * (np.exp(outputs[1])-1)
+```
+
+## 2. Pseudocode for loading models in .tar format
+
+(1) First untar the directory as follows `tar -xvf model.tar`. \
+(2) Use the code below in python after appropriately defining `model_dir_untared` and `inputs`. \
+(3) `inputs` is a one hot encoded sequence of shape (N,2114,4). Here N corresponds to the number
+of tested sequences, 2114 is the input sequence length and 4 corresponds to ACGT.
+
+Reference: https://www.tensorflow.org/api_docs/python/tf/saved_model/load
+
+```python
+import tensorflow as tf
+
+model = tf.saved_model.load('model_dir_untared')
+outputs = model.signatures['serving_default'](**{'sequence':inputs.astype('float32')})
+```
+
+The variable `outputs` represents a dictionary containing two key-value pairs. The first key
+is `logits_profile_predictions`, holding a value with a shape of (N, 1000). This value corresponds
+to logit predictions for a 1000-base-pair output. The second key, named `logcount_predictions``, 
+is associated with a value of shape (N, 1), representing logcount predictions. To transform these
+predictions into per-base signals, utilize the provided pseudo code lines mentioned below.
+
+```python
+import numpy as np
+def softmax(x, temp=1):
+    norm_x = x - np.mean(x,axis=1, keepdims=True)
+    return np.exp(temp*norm_x)/np.sum(np.exp(temp*norm_x), axis=1, keepdims=True)
+    
+predictions = softmax(outputs["logits_profile_predictions"]) * (np.exp(outputs["logcount_predictions"])-1)
+```
+
+## Docker image to load and use the models
+- https://hub.docker.com/r/kundajelab/chrombpnet-atlas/ (tag:v1)
+
+## Code for ChromBPNet
+- https://github.com/kundajelab/chrombpnet/
+
+# License & citation
+External data users may freely download, analyze and publish results based on any ENCODE data without restrictions.
+
+Released under the [ENCODE data-use policy](https://www.encodeproject.org/about/data-use-policy/). Please cite the ENCODE Project Consortium and the model software: [ChromBPNet](https://github.com/kundajelab/chrombpnet) (Pampari et al., bioRxiv 2024).

fold_0/logs.models.fold_0.ENCSR866ODX/logfile.modelling.fold_0.ENCSR866ODX.args.json

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+{
+    "genome": "/scratch/groups/akundaje/anusri/chromatin_atlas/reference/hg38.genome.fa",
+    "bigwig": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR866ODX//preprocessing/bigWigs/ENCSR866ODX.bigWig",
+    "peaks": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR866ODX//chrombpnet_model_encsr880cub_bias//filtered.peaks.bed",
+    "nonpeaks": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR866ODX//chrombpnet_model_encsr880cub_bias//filtered.nonpeaks.bed",
+    "output_prefix": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR866ODX//chrombpnet_model_encsr880cub_bias//chrombpnet",
+    "chr_fold_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_0.json",
+    "trackables": [
+        "logcount_predictions_loss",
+        "loss",
+        "logits_profile_predictions_loss",
+        "val_logcount_predictions_loss",
+        "val_loss",
+        "val_logits_profile_predictions_loss"
+    ],
+    "epochs": 50,
+    "early_stop": 5,
+    "batch_size": 64,
+    "learning_rate": 0.001,
+    "params": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR866ODX//chrombpnet_model_encsr880cub_bias//chrombpnet_model_params.tsv",
+    "seed": 1234,
+    "architecture_from_file": "/home/users/anusri/chromatin-atlas-anvil/sherlock/chrombpnet/src/training/models/chrombpnet_with_bias_model.py"
+}

fold_0/logs.models.fold_0.ENCSR866ODX/logfile.modelling.fold_0.ENCSR866ODX.bias_formatting.stderr.txt

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+INFO:    underlay of /etc/localtime required more than 50 (88) bind mounts
+INFO:    underlay of /usr/bin/nvidia-smi required more than 50 (355) bind mounts
+2023-07-15 02:38:19.792622: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 02:38:25.351798: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-15 02:38:25.357719: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
+2023-07-15 02:38:25.385279: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties: 
+pciBusID: 0000:03:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
+coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
+2023-07-15 02:38:25.385348: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 02:38:25.457582: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
+2023-07-15 02:38:25.457755: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
+2023-07-15 02:38:25.475500: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-15 02:38:25.559487: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-15 02:38:25.624277: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-15 02:38:25.643591: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
+2023-07-15 02:38:25.646693: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
+2023-07-15 02:38:25.648910: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-15 02:38:25.649273: 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
+To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
+2023-07-15 02:38:25.649389: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-15 02:38:25.649643: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties: 
+pciBusID: 0000:03:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
+coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
+2023-07-15 02:38:25.649683: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 02:38:25.649711: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
+2023-07-15 02:38:25.649736: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
+2023-07-15 02:38:25.649762: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-15 02:38:25.649787: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-15 02:38:25.649811: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-15 02:38:25.649835: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
+2023-07-15 02:38:25.649860: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
+2023-07-15 02:38:25.650228: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-15 02:38:25.652380: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 02:38:28.811998: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
+2023-07-15 02:38:28.812116: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267]      0 
+2023-07-15 02:38:28.812135: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0:   N 
+2023-07-15 02:38:28.815107: 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: 0000:03:00.0, compute capability: 6.0)
+2023-07-15 02:38:29.678896: 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.ENCSR866ODX/logfile.modelling.fold_0.ENCSR866ODX.bias_formatting.stdout.txt

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+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//ENCSR866ODX//chrombpnet_model_encsr880cub_bias/bias_model_scaled.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR866ODX//chrombpnet_model_encsr880cub_bias/new_model_formats/bias_model_scaled

fold_0/logs.models.fold_0.ENCSR866ODX/logfile.modelling.fold_0.ENCSR866ODX.chrombpnet.params.json

@@ -0,0 +1,11 @@
+{
+    "counts_loss_weight": "26.8",
+    "filters": "512",
+    "n_dil_layers": "8",
+    "bias_model_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR866ODX//chrombpnet_model_encsr880cub_bias/bias_model_scaled.h5",
+    "inputlen": "2114",
+    "outputlen": "1000",
+    "max_jitter": "500",
+    "chr_fold_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_0.json",
+    "negative_sampling_ratio": "0.1"
+}

fold_0/logs.models.fold_0.ENCSR866ODX/logfile.modelling.fold_0.ENCSR866ODX.chrombpnet_data_params.tsv

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+counts_sum_min_thresh	10.0
+counts_sum_max_thresh	5146.47
+trainings_pts_post_thresh	169685

fold_0/logs.models.fold_0.ENCSR866ODX/logfile.modelling.fold_0.ENCSR866ODX.chrombpnet_formatting.stderr.txt

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+INFO:    underlay of /etc/localtime required more than 50 (88) bind mounts
+INFO:    underlay of /usr/bin/nvidia-smi required more than 50 (355) bind mounts
+2023-07-15 01:38:26.435861: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 01:38:29.565974: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-15 01:38:29.570796: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
+2023-07-15 01:38:29.625707: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties: 
+pciBusID: 0000:82:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
+coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
+2023-07-15 01:38:29.625840: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 01:38:29.654955: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
+2023-07-15 01:38:29.655139: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
+2023-07-15 01:38:29.669432: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-15 01:38:29.675823: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-15 01:38:29.698542: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-15 01:38:29.704203: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
+2023-07-15 01:38:29.705426: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
+2023-07-15 01:38:29.711359: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-15 01:38:29.711799: 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
+To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
+2023-07-15 01:38:29.712723: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-15 01:38:29.730600: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties: 
+pciBusID: 0000:82:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
+coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
+2023-07-15 01:38:29.730738: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 01:38:29.730812: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
+2023-07-15 01:38:29.730846: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
+2023-07-15 01:38:29.730877: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-15 01:38:29.730908: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-15 01:38:29.730938: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-15 01:38:29.730978: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
+2023-07-15 01:38:29.731007: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
+2023-07-15 01:38:29.731596: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-15 01:38:29.732965: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 01:38:31.578748: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
+2023-07-15 01:38:31.578864: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267]      0 
+2023-07-15 01:38:31.578885: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0:   N 
+2023-07-15 01:38:31.582131: 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)
+2023-07-15 01:38:34.021135: 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.
+/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.
+  , UserWarning)

fold_0/logs.models.fold_0.ENCSR866ODX/logfile.modelling.fold_0.ENCSR866ODX.chrombpnet_formatting.stdout.txt

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+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//ENCSR866ODX//chrombpnet_model_encsr880cub_bias/chrombpnet.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR866ODX//chrombpnet_model_encsr880cub_bias/new_model_formats/chrombpnet

fold_0/logs.models.fold_0.ENCSR866ODX/logfile.modelling.fold_0.ENCSR866ODX.chrombpnet_model_params.tsv

@@ -0,0 +1,9 @@
+counts_loss_weight	26.8
+filters	512
+n_dil_layers	8
+bias_model_path	/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR866ODX//chrombpnet_model_encsr880cub_bias/bias_model_scaled.h5
+inputlen	2114
+outputlen	1000
+max_jitter	500
+chr_fold_path	/scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_0.json
+negative_sampling_ratio	0.1

fold_0/logs.models.fold_0.ENCSR866ODX/logfile.modelling.fold_0.ENCSR866ODX.chrombpnet_no_bias_formatting.stderr.txt

@@ -0,0 +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//ENCSR866ODX//chrombpnet_model_encsr880cub_bias/chrombpnet_wo_bias.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR866ODX//chrombpnet_model_encsr880cub_bias/new_model_formats/chrombpnet_wo_bias

fold_0/logs.models.fold_0.ENCSR866ODX/logfile.modelling.fold_0.ENCSR866ODX.chrombpnet_no_bias_formatting.stdout.txt

@@ -0,0 +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//ENCSR866ODX//chrombpnet_model_encsr880cub_bias/chrombpnet_wo_bias.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR866ODX//chrombpnet_model_encsr880cub_bias/new_model_formats/chrombpnet_wo_bias

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fold_0/model.chrombpnet_nobias.fold_0.ENCSR866ODX.h5

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fold_1/logs.models.fold_1.ENCSR866ODX/logfile.modelling.fold_1.ENCSR866ODX.args.json

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+{
+    "genome": "/scratch/groups/akundaje/anusri/chromatin_atlas/reference/hg38.genome.fa",
+    "bigwig": "/oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR866ODX//preprocessing/bigWigs/ENCSR866ODX.bigWig",
+    "peaks": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_1//filtered.peaks.bed",
+    "nonpeaks": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_1//filtered.nonpeaks.bed",
+    "output_prefix": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_1//chrombpnet",
+    "chr_fold_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_1.json",
+    "trackables": [
+        "logcount_predictions_loss",
+        "loss",
+        "logits_profile_predictions_loss",
+        "val_logcount_predictions_loss",
+        "val_loss",
+        "val_logits_profile_predictions_loss"
+    ],
+    "epochs": 50,
+    "early_stop": 5,
+    "batch_size": 64,
+    "learning_rate": 0.001,
+    "params": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_1//chrombpnet_model_params.tsv",
+    "seed": 1234,
+    "architecture_from_file": "/home/users/anusri/chromatin-atlas-anvil/sherlock/chrombpnet/src/training/models/chrombpnet_with_bias_model.py"
+}

fold_1/logs.models.fold_1.ENCSR866ODX/logfile.modelling.fold_1.ENCSR866ODX.bias_formatting.stderr.txt

@@ -0,0 +1,38 @@
+INFO:    underlay of /etc/localtime required more than 50 (88) bind mounts
+INFO:    underlay of /usr/bin/nvidia-smi required more than 50 (355) bind mounts
+2023-07-15 02:38:19.792826: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 02:38:25.418646: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-15 02:38:25.425184: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
+2023-07-15 02:38:25.457408: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties: 
+pciBusID: 0000:82:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
+coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
+2023-07-15 02:38:25.457530: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 02:38:25.490510: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
+2023-07-15 02:38:25.490649: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
+2023-07-15 02:38:25.507882: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-15 02:38:25.559574: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-15 02:38:25.624905: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-15 02:38:25.644854: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
+2023-07-15 02:38:25.646795: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
+2023-07-15 02:38:25.649713: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-15 02:38:25.650201: 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
+To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
+2023-07-15 02:38:25.651405: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-15 02:38:25.651914: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties: 
+pciBusID: 0000:82:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
+coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
+2023-07-15 02:38:25.651965: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 02:38:25.652014: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
+2023-07-15 02:38:25.652060: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
+2023-07-15 02:38:25.652103: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-15 02:38:25.652146: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-15 02:38:25.652189: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-15 02:38:25.652232: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
+2023-07-15 02:38:25.652275: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
+2023-07-15 02:38:25.653299: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-15 02:38:25.655050: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 02:38:28.919480: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
+2023-07-15 02:38:28.919577: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267]      0 
+2023-07-15 02:38:28.919597: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0:   N 
+2023-07-15 02:38:28.922712: 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)
+2023-07-15 02:38:29.813250: 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_1/logs.models.fold_1.ENCSR866ODX/logfile.modelling.fold_1.ENCSR866ODX.bias_formatting.stdout.txt

@@ -0,0 +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//ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_1/bias_model_scaled.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_1/new_model_formats/bias_model_scaled

fold_1/logs.models.fold_1.ENCSR866ODX/logfile.modelling.fold_1.ENCSR866ODX.chrombpnet.params.json

@@ -0,0 +1,11 @@
+{
+    "counts_loss_weight": "26.8",
+    "filters": "512",
+    "n_dil_layers": "8",
+    "bias_model_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_1/bias_model_scaled.h5",
+    "inputlen": "2114",
+    "outputlen": "1000",
+    "max_jitter": "500",
+    "chr_fold_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_1.json",
+    "negative_sampling_ratio": "0.1"
+}

fold_1/logs.models.fold_1.ENCSR866ODX/logfile.modelling.fold_1.ENCSR866ODX.chrombpnet_data_params.tsv

@@ -0,0 +1,3 @@
+counts_sum_min_thresh	12.0
+counts_sum_max_thresh	5197.41
+trainings_pts_post_thresh	171332

fold_1/logs.models.fold_1.ENCSR866ODX/logfile.modelling.fold_1.ENCSR866ODX.chrombpnet_formatting.stderr.txt

@@ -0,0 +1,40 @@
+INFO:    underlay of /etc/localtime required more than 50 (88) bind mounts
+INFO:    underlay of /usr/bin/nvidia-smi required more than 50 (355) bind mounts
+2023-07-15 01:38:26.721162: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 01:38:29.807306: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-15 01:38:29.811764: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
+2023-07-15 01:38:29.844424: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties: 
+pciBusID: 0000:04:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
+coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
+2023-07-15 01:38:29.844515: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 01:38:29.871935: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
+2023-07-15 01:38:29.872094: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
+2023-07-15 01:38:29.886573: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-15 01:38:29.893517: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-15 01:38:29.917075: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-15 01:38:29.922933: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
+2023-07-15 01:38:29.924182: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
+2023-07-15 01:38:29.925962: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-15 01:38:29.926317: 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
+To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
+2023-07-15 01:38:29.927206: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-15 01:38:29.927494: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties: 
+pciBusID: 0000:04:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
+coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
+2023-07-15 01:38:29.927533: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 01:38:29.927558: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
+2023-07-15 01:38:29.927581: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
+2023-07-15 01:38:29.927603: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-15 01:38:29.927625: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-15 01:38:29.927646: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-15 01:38:29.927668: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
+2023-07-15 01:38:29.927690: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
+2023-07-15 01:38:29.928066: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-15 01:38:29.929432: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 01:38:31.747913: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
+2023-07-15 01:38:31.748010: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267]      0 
+2023-07-15 01:38:31.748030: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0:   N 
+2023-07-15 01:38:31.751058: 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)
+2023-07-15 01:38:34.108022: 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.
+/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.
+  , UserWarning)

fold_1/logs.models.fold_1.ENCSR866ODX/logfile.modelling.fold_1.ENCSR866ODX.chrombpnet_formatting.stdout.txt

@@ -0,0 +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//ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_1/chrombpnet.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_1/new_model_formats/chrombpnet

fold_1/logs.models.fold_1.ENCSR866ODX/logfile.modelling.fold_1.ENCSR866ODX.chrombpnet_model_params.tsv

@@ -0,0 +1,9 @@
+counts_loss_weight	26.8
+filters	512
+n_dil_layers	8
+bias_model_path	/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_1/bias_model_scaled.h5
+inputlen	2114
+outputlen	1000
+max_jitter	500
+chr_fold_path	/scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_1.json
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fold_1/logs.models.fold_1.ENCSR866ODX/logfile.modelling.fold_1.ENCSR866ODX.chrombpnet_no_bias_formatting.stderr.txt

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+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//ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_1/chrombpnet_wo_bias.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_1/new_model_formats/chrombpnet_wo_bias

fold_1/logs.models.fold_1.ENCSR866ODX/logfile.modelling.fold_1.ENCSR866ODX.chrombpnet_no_bias_formatting.stdout.txt

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+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//ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_1/chrombpnet_wo_bias.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_1/new_model_formats/chrombpnet_wo_bias

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fold_2/logs.models.fold_2.ENCSR866ODX/logfile.modelling.fold_2.ENCSR866ODX.args.json

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+{
+    "genome": "/scratch/groups/akundaje/anusri/chromatin_atlas/reference/hg38.genome.fa",
+    "bigwig": "/oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR866ODX//preprocessing/bigWigs/ENCSR866ODX.bigWig",
+    "peaks": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_2//filtered.peaks.bed",
+    "nonpeaks": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_2//filtered.nonpeaks.bed",
+    "output_prefix": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_2//chrombpnet",
+    "chr_fold_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_2.json",
+    "trackables": [
+        "logcount_predictions_loss",
+        "loss",
+        "logits_profile_predictions_loss",
+        "val_logcount_predictions_loss",
+        "val_loss",
+        "val_logits_profile_predictions_loss"
+    ],
+    "epochs": 50,
+    "early_stop": 5,
+    "batch_size": 64,
+    "learning_rate": 0.001,
+    "params": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_2//chrombpnet_model_params.tsv",
+    "seed": 1234,
+    "architecture_from_file": "/home/users/anusri/chromatin-atlas-anvil/sherlock/chrombpnet/src/training/models/chrombpnet_with_bias_model.py"
+}

fold_2/logs.models.fold_2.ENCSR866ODX/logfile.modelling.fold_2.ENCSR866ODX.bias_formatting.stderr.txt

@@ -0,0 +1,38 @@
+INFO:    underlay of /etc/localtime required more than 50 (88) bind mounts
+INFO:    underlay of /usr/bin/nvidia-smi required more than 50 (355) bind mounts
+2023-07-15 02:38:19.792933: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 02:38:25.380703: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-15 02:38:25.385810: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
+2023-07-15 02:38:25.411618: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties: 
+pciBusID: 0000:04:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
+coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
+2023-07-15 02:38:25.411728: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 02:38:25.457879: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
+2023-07-15 02:38:25.457992: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
+2023-07-15 02:38:25.476744: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-15 02:38:25.559890: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-15 02:38:25.629823: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-15 02:38:25.646246: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
+2023-07-15 02:38:25.648184: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
+2023-07-15 02:38:25.650848: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-15 02:38:25.651292: 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
+To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
+2023-07-15 02:38:25.652728: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-15 02:38:25.653425: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties: 
+pciBusID: 0000:04:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
+coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
+2023-07-15 02:38:25.653474: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 02:38:25.653520: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
+2023-07-15 02:38:25.653559: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
+2023-07-15 02:38:25.653597: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-15 02:38:25.653634: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-15 02:38:25.653680: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-15 02:38:25.653720: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
+2023-07-15 02:38:25.653757: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
+2023-07-15 02:38:25.654334: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-15 02:38:25.656486: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 02:38:28.965930: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
+2023-07-15 02:38:28.966041: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267]      0 
+2023-07-15 02:38:28.966060: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0:   N 
+2023-07-15 02:38:28.969323: 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)
+2023-07-15 02:38:29.808077: 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.ENCSR866ODX/logfile.modelling.fold_2.ENCSR866ODX.bias_formatting.stdout.txt

@@ -0,0 +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//ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_2/bias_model_scaled.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_2/new_model_formats/bias_model_scaled

fold_2/logs.models.fold_2.ENCSR866ODX/logfile.modelling.fold_2.ENCSR866ODX.chrombpnet.params.json

@@ -0,0 +1,11 @@
+{
+    "counts_loss_weight": "26.8",
+    "filters": "512",
+    "n_dil_layers": "8",
+    "bias_model_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_2/bias_model_scaled.h5",
+    "inputlen": "2114",
+    "outputlen": "1000",
+    "max_jitter": "500",
+    "chr_fold_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_2.json",
+    "negative_sampling_ratio": "0.1"
+}

fold_2/logs.models.fold_2.ENCSR866ODX/logfile.modelling.fold_2.ENCSR866ODX.chrombpnet_data_params.tsv

@@ -0,0 +1,3 @@
+counts_sum_min_thresh	12.0
+counts_sum_max_thresh	5151.0
+trainings_pts_post_thresh	177254

fold_2/logs.models.fold_2.ENCSR866ODX/logfile.modelling.fold_2.ENCSR866ODX.chrombpnet_formatting.stderr.txt

@@ -0,0 +1,40 @@
+INFO:    underlay of /etc/localtime required more than 50 (88) bind mounts
+INFO:    underlay of /usr/bin/nvidia-smi required more than 50 (355) bind mounts
+2023-07-15 01:38:26.471086: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 01:38:29.465809: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-15 01:38:29.471055: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
+2023-07-15 01:38:29.499029: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties: 
+pciBusID: 0000:83:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
+coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
+2023-07-15 01:38:29.499145: 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 01:38:29.542960: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
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+2023-07-15 01:38:29.573549: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-15 01:38:29.579782: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
+2023-07-15 01:38:29.581028: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
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+To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
+2023-07-15 01:38:29.592917: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-15 01:38:29.593309: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties: 
+pciBusID: 0000:83:00.0 name: Tesla P100-PCIE-16GB computeCapability: 6.0
+coreClock: 1.3285GHz coreCount: 56 deviceMemorySize: 15.89GiB deviceMemoryBandwidth: 681.88GiB/s
+2023-07-15 01:38:29.593342: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 01:38:29.593377: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
+2023-07-15 01:38:29.593405: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
+2023-07-15 01:38:29.593431: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-15 01:38:29.593455: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-15 01:38:29.593480: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-15 01:38:29.593505: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
+2023-07-15 01:38:29.593529: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
+2023-07-15 01:38:29.608416: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-15 01:38:29.609818: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-15 01:38:31.460622: 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 01:38:31.460764: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0:   N 
+2023-07-15 01:38:31.463809: 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)
+2023-07-15 01:38:33.810724: 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.
+/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.
+  , UserWarning)

fold_2/logs.models.fold_2.ENCSR866ODX/logfile.modelling.fold_2.ENCSR866ODX.chrombpnet_formatting.stdout.txt

@@ -0,0 +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//ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_2/chrombpnet.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR866ODX//chrombppnet_model_encsr880cub_bias_fold_2/new_model_formats/chrombpnet