Attribute error about spliceai HOT 4 CLOSED

I believe you're using an older version of SpliceAI, please use the latest one (1.3.1, where get_values has been replaced with to_numpy).

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Thanks for the quick reply, i have updated it to newer version. But it worked for few minutes and crashed, here is the log file i have

2020-06-15 08:51:12.953875: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcublas.so.10
2020-06-15 08:51:13.050069: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcufft.so.10
2020-06-15 08:51:13.192566: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcurand.so.10
2020-06-15 08:51:13.334814: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcusolver.so.10
2020-06-15 08:51:13.412529: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcusparse.so.10
2020-06-15 08:51:13.413095: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcudnn.so.7
2020-06-15 08:51:13.417279: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1697] Adding visible gpu devices: 0
2020-06-15 08:51:13.418690: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 AVX512F FMA
2020-06-15 08:51:13.436570: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2400000000 Hz
2020-06-15 08:51:13.437177: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x654c460 initialized for platform Host (this does not guarantee that XLA will be used). Devices:
2020-06-15 08:51:13.437229: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version
2020-06-15 08:51:13.813090: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x65ba360 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:
2020-06-15 08:51:13.813245: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Tesla V100-SXM2-16GB, Compute Capability 7.0
2020-06-15 08:51:13.815621: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1555] Found device 0 with properties:
pciBusID: 0000:1a:00.0 name: Tesla V100-SXM2-16GB computeCapability: 7.0
coreClock: 1.53GHz coreCount: 80 deviceMemorySize: 15.75GiB deviceMemoryBandwidth: 836.37GiB/s
2020-06-15 08:51:13.815900: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcudart.so.10.1
2020-06-15 08:51:13.815925: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcublas.so.10
2020-06-15 08:51:13.815976: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcufft.so.10
2020-06-15 08:51:13.815997: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcurand.so.10
2020-06-15 08:51:13.816018: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcusolver.so.10
2020-06-15 08:51:13.816039: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcusparse.so.10
2020-06-15 08:51:13.816055: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcudnn.so.7
2020-06-15 08:51:13.819456: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1697] Adding visible gpu devices: 0
2020-06-15 08:51:13.819709: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcudart.so.10.1
2020-06-15 08:51:16.846547: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1096] Device interconnect StreamExecutor with strength 1 edge matrix:
2020-06-15 08:51:16.847259: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1102] 0
2020-06-15 08:51:16.847300: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1115] 0: N
2020-06-15 08:51:16.852007: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1241] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 14949 MB memory) -> physical GPU (device: 0, name: Tesla V100-SXM2-16GB, pci bus id: 0000:1a:00.0, compute capability: 7.0)
2020-06-15 08:52:11.982675: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcudnn.so.7
2020-06-15 08:52:21.681460: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcublas.so.10
Using TensorFlow backend.
/usr/local/lib/python3.6/dist-packages/keras/engine/saving.py:341: UserWarning: No training configuration found in save file: the model was not compiled. Compile it manually.
warnings.warn('No training configuration found in save file: '
(END)

Let me know what else I can do for it to work. Thank you.

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There's nothing in the logs suggesting a crash. Could you look at the output and let me know which variant caused this issue? Also, could you try using the examples/input.vcf file as input and see if you can reproduce the examples/output.vcf file as the output?

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Closing due to inactivity, please feel free to reopen if the issue is still valid.

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