Open Shenying71 opened 2 years ago
Licko0909
commented
2 years ago Hi, Shenying71. I suggest that a）you can check the format of the input file (TFRecord) to see if it contains the "sequence" key，because ”Key: sequence. Can't parse serialized Example.“ b）Check whether the environments are consistent (tensorflow-GPU =2.0) and whether the devices support Gpus
Shenying71
commented
2 years ago Hi Licko0909, Thanks so much for your reply! I don't think the issue I reported before was due to the two reasons you suggested. Are there any other reasons?
a) Actually I printed out the TRRecord and it contains "sequence" or "masked_sequence".
import tensorflow as tf
filenames = ["hg19_seq_gram_5_stride_1_slice_200000_0_1_2_3_4.tfrecord"] raw_dataset = tf.data.TFRecordDataset(filenames) raw_dataset
for raw_record in raw_dataset.take(100): example = tf.train.Example() example.ParseFromString(raw_record.numpy()) print(example)
features { feature { key: "masked_sequence" value { int64_list { value: 3107 value: 2 value: 2082 value: 2127 ... value: 2 value: 2634 value: 1763 value: 2383 value: 2631 value: 1809 value: 1773 value: 1320 value: 2784 value: 2892 value: 1262 value: 1259 value: 1519 value: 2289 value: 3130 } } } feature { key: "sequence" value { int64_list { value: 3107 value: 1269 value: 2082 ... value: 3030 value: 3063 value: 2634 value: 1763 value: 2383 value: 2631 value: 1809 value: 1773 value: 1320 value: 2784 value: 2892 value: 1262 value: 1259 value: 1519 value: 2289 value: 3130 } } } }
b) Our Singularity container for TensorFlow does have version 2.0.0:
$ module load tensorflow
Tensorflow is set up as a singularity container.
Use the variable $tf to run our python script.
For example:
$tf /full/path/to/your/pythonsrcipt
at this moment only your /rsrch3/home directory is mounted.
[emsisson@ldragon1 ~]$ module list
Currently Loaded Modules:
1) cuda11.1/toolkit/11.1.1 3) singularity/3.7.0
2) gcc/7.1.0 4) tensorflow/20191220-gpuUbuntu 18.04 gcc 7.5.0
cudatoolkit 10.0.130 0 defaults cudnn 7.6.5 cuda10.0_0 defaults ... keras 2.3.1 0 defaults keras-applications 1.0.8 py_1 defaults keras-base 2.3.1 py36_0 defaults keras-preprocessing 1.1.2 pyhd3eb1b0_0 defaults pandas 1.1.5 py36ha9443f7_0 defaults python 3.6.9 h265db76_0 defaults ... tensorflow 2.0.0 gpu_py36h6b29c10_0 defaults tensorflow-base 2.0.0 gpu_py36h0ec5d1f_0 defaults tensorflow-estimator 2.0.0 pyh2649769_0 defaults tensorflow-gpu 2.0.0 h0d30ee6_0 defaults
1) Close the backend eager, make the following change:
file: LOGO/bgi/bert4keras/backend.py
change:
2) Make the following change: file: LOGO/01_Pre-training_Model/02_run_genebert_bert4keras_tfrecord_train.sh change: stride=1 -> stride=5
The following is an example of the implementation process:
Shenying71
commented
2 years ago Great. Thanks so much Licko0909! The program works now. As I know most DNA transformer projects use stride =1 for k mers(3,4,5,6,7). If we use stride=5 for 5 mers(ngram=5), we may not capture sufficient DNA sequence information compared with using stride=1 ? Can you fix the codes by keeping stride=1? Shenying
Shenying71
commented
2 years ago Hello
Could you please address the following questions (in red text)?
In your LOGO_Variant_Priortization file,
Can you provide codes to streamline the procedure: 1. Generate .npz file from CAD VCF sequence data? 2. Generate .tfrecord files and models; 3 classfication based on models
Data download, see Data_URL.txt, Save to /data/CADD/
Generate vcf sequence (This file only generated .tfrecord files, no .npz files, were those files directly fed into step 4?)
From: Licko0909 @.>
Sent: Saturday, October 9, 2021 2:25 AM
To: melobio/LOGO @.>
Cc: Fang,Shenying @.>; Author @.>
Subject: [EXT] Re: [melobio/LOGO] There is non-GPU devices in tf.distribute.Strategy, not using nccl allreduce (#1)
WARNING: This email originated from outside of MD Anderson. Please validate the sender's email address before clicking on links or attachments as they may not be safe.
First System
Ubuntu 18.04 gcc 7.5.0
Conda environment
cudatoolkit 10.0.130 0 defaults cudnn 7.6.5 cuda10.0_0 defaults ... keras 2.3.1 0 defaults keras-applications 1.0.8 py_1 defaults keras-base 2.3.1 py36_0 defaults keras-preprocessing 1.1.2 pyhd3eb1b0_0 defaults pandas 1.1.5 py36ha9443f7_0 defaults python 3.6.9 h265db76_0 defaults ... tensorflow 2.0.0 gpu_py36h6b29c10_0 defaults tensorflow-base 2.0.0 gpu_py36h0ec5d1f_0 defaults tensorflow-estimator 2.0.0 pyh2649769_0 defaults tensorflow-gpu 2.0.0 h0d30ee6_0 defaults
Second
The following is an example of the implementation process: [image]https://urldefense.com/v3/__https:/user-images.githubusercontent.com/27897166/136648587-5dfa2890-aea7-494b-8aee-296485ce1cb7.png__;!!PfbeBCCAmug!1pn5LCiU2osqjVLeYl9MnRjBwzHLajDCHbWfV2YbRV1jUR119LyaYODn4Ut0jo7O$
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/melobio/LOGO/issues/1*issuecomment-939246764__;Iw!!PfbeBCCAmug!1pn5LCiU2osqjVLeYl9MnRjBwzHLajDCHbWfV2YbRV1jUR119LyaYODn4XUuNGiu$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/ARM7OGA27QJZIQQVYMDHS3DUF7U6PANCNFSM5FKGBXQA__;!!PfbeBCCAmug!1pn5LCiU2osqjVLeYl9MnRjBwzHLajDCHbWfV2YbRV1jUR119LyaYODn4d3zUhvW$. Triage notifications on the go with GitHub Mobile for iOShttps://urldefense.com/v3/__https:/apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675__;!!PfbeBCCAmug!1pn5LCiU2osqjVLeYl9MnRjBwzHLajDCHbWfV2YbRV1jUR119LyaYODn4cnrKXPy$ or Androidhttps://urldefense.com/v3/__https:/play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign*3Dnotification-email*26utm_medium*3Demail*26utm_source*3Dgithub__;JSUlJSU!!PfbeBCCAmug!1pn5LCiU2osqjVLeYl9MnRjBwzHLajDCHbWfV2YbRV1jUR119LyaYODn4fdIRqw0$.
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Shenying71
commented
2 years ago Hello,
When I ran the model “02_cadd_classification_transformer_tfrecord.py” for cadd data, I used the following data and ran into error messages: can’t parse serialized example. Can you provide help?
train_slice_files = [ '/rsrch3/home/surgonc_rsrch/sfang/LOGO/LOGO-master/05_LOGO_Variant_Prioritization/CADD/GRCh37/SNVS1/humanDerived_SNVs_gram_5_stride_1_slice_100000_100000_train.tfrecord','/rsrch3/home/surgonc_rsrch/sfang/LOGO/LOGO-master/05_LOGO_Variant_Prioritization/CADD/GRCh37/SNVS1/humanDerived_SNVs_gram_5_stride_1_slice_200000_200000_train.tfrecord' ] valid_slice_files = [ '/rsrch3/home/surgonc_rsrch/sfang/LOGO/LOGO-master/05_LOGO_Variant_Prioritization/CADD/GRCh37/SNVS1/humanDerived_SNVs_gram_5_stride_1_slice_100000_100000_valid.tfrecord' ] test_slice_files = [ '/rsrch3/home/surgonc_rsrch/sfang/LOGO/LOGO-master/05_LOGO_Variant_Prioritization/CADD/GRCh37/SNVS1/humanDerived_SNVs_gram_5_stride_1_slice_100000_100000_test.tfrecord' ]
train_total_size =180000
valid_total_size = 5000
test_total_size = 5000I ran into the following errors:
Train on 175 steps, validate on 2 steps
Epoch 1/100
2021-10-25 21:11:09.434153: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_seq. Can't parse serialized Example.
2021-10-25 21:11:09.434270: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_seq. Can't parse serialized Example.
Traceback (most recent call last):
File "02_cadd_classification_transformer_tfrecord.py", line 278, in
Sent: Saturday, October 9, 2021 2:25 AM
To: melobio/LOGO @.>
Cc: Fang,Shenying @.>; Author @.***>
Subject: [EXT] Re: [melobio/LOGO] There is non-GPU devices in tf.distribute.Strategy, not using nccl allreduce (#1)
WARNING: This email originated from outside of MD Anderson. Please validate the sender's email address before clicking on links or attachments as they may not be safe.
First System
Ubuntu 18.04 gcc 7.5.0
Conda environment
cudatoolkit 10.0.130 0 defaults cudnn 7.6.5 cuda10.0_0 defaults ... keras 2.3.1 0 defaults keras-applications 1.0.8 py_1 defaults keras-base 2.3.1 py36_0 defaults keras-preprocessing 1.1.2 pyhd3eb1b0_0 defaults pandas 1.1.5 py36ha9443f7_0 defaults python 3.6.9 h265db76_0 defaults ... tensorflow 2.0.0 gpu_py36h6b29c10_0 defaults tensorflow-base 2.0.0 gpu_py36h0ec5d1f_0 defaults tensorflow-estimator 2.0.0 pyh2649769_0 defaults tensorflow-gpu 2.0.0 h0d30ee6_0 defaults
Second
The following is an example of the implementation process: [image]https://urldefense.com/v3/__https:/user-images.githubusercontent.com/27897166/136648587-5dfa2890-aea7-494b-8aee-296485ce1cb7.png__;!!PfbeBCCAmug!1pn5LCiU2osqjVLeYl9MnRjBwzHLajDCHbWfV2YbRV1jUR119LyaYODn4Ut0jo7O$
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The following have been reloaded with a version change: 1) gcc/7.2.0 => gcc/7.1.0
Using TensorFlow backend. WARNING:tensorflow:There is non-GPU devices in
tf.distribute.Strategy, not using nccl allreduce. WARNING:tensorflow:From ../bgi/bert4keras/models.py:179: The name tf.keras.initializers.TruncatedNormal is deprecated. Please use tf.compat.v1.keras.initializers.TruncatedNormal instead.WARNING:tensorflow:From /risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/keras/initializers.py:94: calling TruncatedNormal.init (from tensorflow.python.ops.init_ops) with dtype is deprecated and will be removed in a future version. Instructions for updating: Call initializer instance with the dtype argument instead of passing it to the constructor WARNING:tensorflow:From /risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/ops/resource_variable_ops.py:1630: calling BaseResourceVariable.init (from tensorflow.python.ops.resource_variable_ops) with constraint is deprecated and will be removed in a future version. Instructions for updating: If using Keras pass *_constraint arguments to layers. WARNING:tensorflow:From /risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/ops/math_grad.py:1424: where (from tensorflow.python.ops.array_ops) is deprecated and will be removed in a future version. Instructions for updating: Use tf.where in 2.0, which has the same broadcast rule as np.where Traceback (most recent call last): File "02_train_gene_transformer_lm_hg_bert4keras_tfrecord.py", line 339, in
verbose=1
File "/risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/keras/engine/training.py", line 727, in fit
use_multiprocessing=use_multiprocessing)
File "/risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/keras/engine/training_distributed.py", line 685, in fit
steps_name='steps_per_epoch')
File "/risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/keras/engine/training_arrays.py", line 300, in model_iteration
batch_outs = f(actual_inputs)
File "/risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/keras/backend.py", line 3476, in call
run_metadata=self.run_metadata)
File "/risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/client/session.py", line 1472, in call
run_metadata_ptr)
tensorflow.python.framework.errors_impl.InvalidArgumentError: {{function_node __inference_Dataset_map_parse_function_2564}} Key: sequence. Can't parse serialized Example.
[[{{node ParseSingleExample/ParseSingleExample}}]]
[[MultiDeviceIteratorGetNextFromShard]]
[[RemoteCall]]
[[IteratorGetNext]]