Add files using upload-large-folder tool

fold_0/logs.models.fold_0.ENCSR799MAX/logfile.modelling.fold_0.ENCSR799MAX.args.json

@@ -0,0 +1,23 @@
+{
+    "genome": "reference/hg38.genome.fa",
+    "bigwig": "data/ENCSR799MAX.bigWig",
+    "peaks": "chrombppnet_model_encsr283tme_bias//filtered.peaks.bed",
+    "nonpeaks": "chrombppnet_model_encsr283tme_bias//filtered.nonpeaks.bed",
+    "output_prefix": "chrombppnet_model_encsr283tme_bias//chrombpnet",
+    "chr_fold_path": "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": "chrombppnet_model_encsr283tme_bias//chrombpnet_model_params.tsv",
+    "seed": 1234,
+    "architecture_from_file": "/scratch/chrombpnet/src/training/models/chrombpnet_with_bias_model.py"
+}

fold_0/logs.models.fold_0.ENCSR799MAX/logfile.modelling.fold_0.ENCSR799MAX.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
+2023-07-17 00:22:01.763648: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-17 00:22:05.352416: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-17 00:22:05.357249: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
+2023-07-17 00:22:05.422296: 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
+2023-07-17 00:22:05.422418: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-17 00:22:05.453123: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
+2023-07-17 00:22:05.453299: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
+2023-07-17 00:22:05.468539: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-17 00:22:05.475508: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-17 00:22:05.503935: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-17 00:22:05.510739: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
+2023-07-17 00:22:05.512280: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
+2023-07-17 00:22:05.528738: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-17 00:22:05.529208: 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.
+2023-07-17 00:22:05.530281: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-17 00:22:05.547835: 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
+2023-07-17 00:22:05.547963: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-17 00:22:05.548027: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
+2023-07-17 00:22:05.548054: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
+2023-07-17 00:22:05.548079: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-17 00:22:05.548103: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-17 00:22:05.548127: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-17 00:22:05.548152: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
+2023-07-17 00:22:05.548176: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
+2023-07-17 00:22:05.549733: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-17 00:22:05.551343: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-17 00:22:07.744391: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
+2023-07-17 00:22:07.744519: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267]      0 
+2023-07-17 00:22:07.744540: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0:   N 
+2023-07-17 00:22:07.748092: 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)
+2023-07-17 00:22:08.777241: 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.ENCSR799MAX/logfile.modelling.fold_0.ENCSR799MAX.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//ENCSR799MAX//chrombppnet_model_encsr283tme_bias/bias_model_scaled.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR799MAX//chrombppnet_model_encsr283tme_bias/new_model_formats/bias_model_scaled

fold_0/logs.models.fold_0.ENCSR799MAX/logfile.modelling.fold_0.ENCSR799MAX.chrombpnet.params.json

@@ -0,0 +1,11 @@
+{
+    "counts_loss_weight": "2.4",
+    "filters": "512",
+    "n_dil_layers": "8",
+    "bias_model_path": "chrombppnet_model_encsr283tme_bias/bias_model_scaled.h5",
+    "inputlen": "2114",
+    "outputlen": "1000",
+    "max_jitter": "500",
+    "chr_fold_path": "splits/fold_0.json",
+    "negative_sampling_ratio": "0.1"
+}

fold_0/logs.models.fold_0.ENCSR799MAX/logfile.modelling.fold_0.ENCSR799MAX.chrombpnet_data_params.tsv

@@ -0,0 +1,3 @@
+counts_sum_min_thresh	0.0
+counts_sum_max_thresh	1336.0
+trainings_pts_post_thresh	145921

fold_0/logs.models.fold_0.ENCSR799MAX/logfile.modelling.fold_0.ENCSR799MAX.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
+2023-07-17 13:48:38.901494: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-17 13:48:42.050600: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-17 13:48:42.055833: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
+2023-07-17 13:48:42.088990: 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
+2023-07-17 13:48:42.089085: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-17 13:48:42.117714: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
+2023-07-17 13:48:42.117829: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
+2023-07-17 13:48:42.131572: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-17 13:48:42.137711: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-17 13:48:42.159913: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-17 13:48:42.165772: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
+2023-07-17 13:48:42.166973: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
+2023-07-17 13:48:42.168947: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-17 13:48:42.169290: 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.
+2023-07-17 13:48:42.170259: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-17 13:48:42.170543: 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
+2023-07-17 13:48:42.170575: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-17 13:48:42.170614: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
+2023-07-17 13:48:42.170636: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
+2023-07-17 13:48:42.170658: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-17 13:48:42.170680: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-17 13:48:42.170702: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-17 13:48:42.170724: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
+2023-07-17 13:48:42.170745: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
+2023-07-17 13:48:42.171103: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-17 13:48:42.172521: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-17 13:48:44.081992: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
+2023-07-17 13:48:44.082095: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267]      0 
+2023-07-17 13:48:44.082113: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0:   N 
+2023-07-17 13:48:44.085177: 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)
+2023-07-17 13:48:46.615235: 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.ENCSR799MAX/logfile.modelling.fold_0.ENCSR799MAX.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//ENCSR799MAX//chrombppnet_model_encsr283tme_bias/chrombpnet.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR799MAX//chrombppnet_model_encsr283tme_bias/new_model_formats/chrombpnet

fold_0/logs.models.fold_0.ENCSR799MAX/logfile.modelling.fold_0.ENCSR799MAX.chrombpnet_model_params.tsv

@@ -0,0 +1,9 @@
+counts_loss_weight	2.4
+filters	512
+n_dil_layers	8
+bias_model_path	chrombppnet_model_encsr283tme_bias/bias_model_scaled.h5
+inputlen	2114
+outputlen	1000
+max_jitter	500
+chr_fold_path	splits/fold_0.json
+negative_sampling_ratio	0.1

fold_0/logs.models.fold_0.ENCSR799MAX/logfile.modelling.fold_0.ENCSR799MAX.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//ENCSR799MAX//chrombppnet_model_encsr283tme_bias/chrombpnet_wo_bias.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR799MAX//chrombppnet_model_encsr283tme_bias/new_model_formats/chrombpnet_wo_bias

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fold_2/logs.models.fold_2.ENCSR799MAX/logfile.modelling.fold_2.ENCSR799MAX.args.json

@@ -0,0 +1,23 @@
+{
+    "genome": "/scratch/groups/akundaje/anusri/chromatin_atlas/reference/hg38.genome.fa",
+    "bigwig": "/oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR799MAX//preprocessing/bigWigs/ENCSR799MAX.bigWig",
+    "peaks": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR799MAX//chrombppnet_model_encsr283tme_bias_fold_2//filtered.peaks.bed",
+    "nonpeaks": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR799MAX//chrombppnet_model_encsr283tme_bias_fold_2//filtered.nonpeaks.bed",
+    "output_prefix": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR799MAX//chrombppnet_model_encsr283tme_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/ENCSR799MAX//chrombppnet_model_encsr283tme_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.ENCSR799MAX/logfile.modelling.fold_2.ENCSR799MAX.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
+2023-07-17 00:22:01.636583: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-17 00:22:05.263058: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-17 00:22:05.268009: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
+2023-07-17 00:22:05.300164: 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
+2023-07-17 00:22:05.300268: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-17 00:22:05.329920: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
+2023-07-17 00:22:05.330085: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
+2023-07-17 00:22:05.345427: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-17 00:22:05.352509: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-17 00:22:05.379395: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-17 00:22:05.386389: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
+2023-07-17 00:22:05.387859: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
+2023-07-17 00:22:05.402550: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-17 00:22:05.403023: 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.
+2023-07-17 00:22:05.404132: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-17 00:22:05.404448: 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
+2023-07-17 00:22:05.404503: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-17 00:22:05.404547: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
+2023-07-17 00:22:05.404572: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
+2023-07-17 00:22:05.404597: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-17 00:22:05.404621: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-17 00:22:05.404645: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-17 00:22:05.404669: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
+2023-07-17 00:22:05.404694: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
+2023-07-17 00:22:05.405102: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-17 00:22:05.406704: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-17 00:22:07.616962: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
+2023-07-17 00:22:07.617078: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267]      0 
+2023-07-17 00:22:07.617099: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0:   N 
+2023-07-17 00:22:07.620621: 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)
+2023-07-17 00:22:08.640883: 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.ENCSR799MAX/logfile.modelling.fold_2.ENCSR799MAX.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//ENCSR799MAX//chrombppnet_model_encsr283tme_bias_fold_2/bias_model_scaled.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR799MAX//chrombppnet_model_encsr283tme_bias_fold_2/new_model_formats/bias_model_scaled

fold_2/logs.models.fold_2.ENCSR799MAX/logfile.modelling.fold_2.ENCSR799MAX.chrombpnet.params.json

@@ -0,0 +1,11 @@
+{
+    "counts_loss_weight": "2.4",
+    "filters": "512",
+    "n_dil_layers": "8",
+    "bias_model_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR799MAX//chrombppnet_model_encsr283tme_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.ENCSR799MAX/logfile.modelling.fold_2.ENCSR799MAX.chrombpnet_data_params.tsv

@@ -0,0 +1,3 @@
+counts_sum_min_thresh	0.0
+counts_sum_max_thresh	1328.0
+trainings_pts_post_thresh	153801

fold_2/logs.models.fold_2.ENCSR799MAX/logfile.modelling.fold_2.ENCSR799MAX.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
+2023-07-17 13:48:38.949046: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-17 13:48:42.089399: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-17 13:48:42.095448: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
+2023-07-17 13:48:42.131176: 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
+2023-07-17 13:48:42.131256: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-17 13:48:42.161779: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
+2023-07-17 13:48:42.161887: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
+2023-07-17 13:48:42.176698: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-17 13:48:42.183254: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-17 13:48:42.210226: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-17 13:48:42.216252: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
+2023-07-17 13:48:42.217537: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
+2023-07-17 13:48:42.220036: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-17 13:48:42.220392: 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.
+2023-07-17 13:48:42.221301: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
+2023-07-17 13:48:42.222234: 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
+2023-07-17 13:48:42.222268: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-17 13:48:42.222302: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
+2023-07-17 13:48:42.222328: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.11
+2023-07-17 13:48:42.222351: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
+2023-07-17 13:48:42.222374: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
+2023-07-17 13:48:42.222396: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
+2023-07-17 13:48:42.222419: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
+2023-07-17 13:48:42.222442: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
+2023-07-17 13:48:42.222806: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
+2023-07-17 13:48:42.224240: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
+2023-07-17 13:48:44.106343: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
+2023-07-17 13:48:44.106413: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267]      0 
+2023-07-17 13:48:44.106431: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0:   N 
+2023-07-17 13:48:44.119702: 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)
+2023-07-17 13:48:46.624360: 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.ENCSR799MAX/logfile.modelling.fold_2.ENCSR799MAX.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//ENCSR799MAX//chrombppnet_model_encsr283tme_bias_fold_2/chrombpnet.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR799MAX//chrombppnet_model_encsr283tme_bias_fold_2/new_model_formats/chrombpnet

fold_2/logs.models.fold_2.ENCSR799MAX/logfile.modelling.fold_2.ENCSR799MAX.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//ENCSR799MAX//chrombppnet_model_encsr283tme_bias_fold_2/chrombpnet_wo_bias.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR799MAX//chrombppnet_model_encsr283tme_bias_fold_2/new_model_formats/chrombpnet_wo_bias

fold_2/logs.models.fold_2.ENCSR799MAX/logfile.modelling.fold_2.ENCSR799MAX.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//ENCSR799MAX//chrombppnet_model_encsr283tme_bias_fold_2/chrombpnet_wo_bias.h5 -o /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR799MAX//chrombppnet_model_encsr283tme_bias_fold_2/new_model_formats/chrombpnet_wo_bias

fold_2/logs.models.fold_2.ENCSR799MAX/logfile.modelling.fold_2.ENCSR799MAX.epoch_loss.csv

@@ -0,0 +1,13 @@
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