8000 CADD prediction-can't parse single sample · Issue #3 · melobio/LOGO · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

CADD prediction-can't parse single sample #3

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ 8000 ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Open
Shenying71 opened this issue Nov 4, 2021 · 0 comments
Open

CADD prediction-can't parse single sample #3

Shenying71 opened this issue Nov 4, 2021 · 0 comments

Comments

@Shenying71
Copy link

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? I would like to apply this process to predict pathogenic effects of somatic variants. Or can you provide revised codes and an example data?

train_slice_files = [
'/rsrch3/home/surgonc_rsrch/sfang/LOGO/LOGO-master/05_LOGO_Variant_Prioritization/CADD/GRCh37/SNVS1/humanDerived_SNVs_gram_5_stride_5_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_5_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_5_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_5_slice_100000_100000_test.tfrecord' ]

        train_total_size =180000
        valid_total_size = 5000
        test_total_size = 5000

I 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
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
2021-10-25 21:11:09.434995: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_type. Can't parse serialized Example.
2021-10-25 21:11:09.435078: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: seq. Can't parse serialized Example.
2021-10-25 21:11:09.435134: 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 21:11:09.435209: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_type. Can't parse serialized Example.
2021-10-25 21:11:09.435261: 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.
use_multiprocessing=use_multiprocessing)
File "/risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/tensorflow_core/python/keras/engine/training_arrays.py", line 675, in fit
2021-10-25 21:11:09.435613: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_type. Can't parse serialized Example.
2021-10-25 21:11:09.435697: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: seq. Can't parse serialized Example.
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
2021-10-25 21:11:09.436015: 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.
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
2021-10-25 21:11:09.436259: 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 21:11:09.436336: 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.
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
2021-10-25 21:11:09.437045: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_type. Can't parse serialized Example.
2021-10-25 21:11:09.437105: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_type. Can't parse serialized Example.
2021-10-25 21:11:09.437173: 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 21:11:09.437225: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: seq. Can't parse serialized Example.
run_metadata_ptr)
tensorflow.python.framework.errors_impl.InvalidArgumentError: {{function_node __inference_Dataset_map_single_example_parser_1272}} Key: alt_seq. Can't parse serialized Example.
[[{{node ParseSingleExample/ParseSingleExample}}]]
[[IteratorGetNext]]
2021-10-25 21:11:09.452867: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: seq. Can't parse serialized Example.
2021-10-25 21:11:09.452934: W tensorflow/core/framework/op_kernel.cc:1651] OP_REQUIRES failed at example_parsing_ops.cc:240 : Invalid argument: Key: alt_type. Can't parse serialized Example.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@Shenying71
0