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Adding checkpoint for step1 and step2 #2

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baozg opened this issue Jun 30, 2022 · 0 comments
Open

Adding checkpoint for step1 and step2 #2

baozg opened this issue Jun 30, 2022 · 0 comments
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enhancement New feature or request

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@baozg
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baozg commented Jun 30, 2022

Hi,

When I use SVision for plant reads-based SV calling, there is some warning. I see this may due to the cluster busy when another task running. It stock more than 12 hours and only have 2 chromosomes vcf in the predict_results. But if I rerun the whole command, it will regenerate the image, I think it can be skipped

SVision -t 32 -o C005_svision -b C005.hifi.sorted.bam -g ref.chr.fa -m ../../../../software/SVision/SVision_CNN/svision-cnn-model.ckpt -n C005 --graph --qname

Log

 WARNING:tensorflow:From /home/baozhigui/software/miniconda3/envs/svisio
n/lib/python3.6/site-packages/tensorflow/python/ops/init_ops.py:1251: calling VarianceScaling.__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 /home/baozhigui/software/miniconda3/envs/svision/lib/python3.6/site-packages/tensorflow/python/ops/init_ops.py:1251: calling VarianceScaling.__init__ (from tensorflow.python.ops.init_ops) with dtype is deprecated a
nd 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 /home/baozhigui/software/miniconda3/envs/svision/lib/python3.6/site-packages/tensorflow/python/ops/init_ops.py:1251: calling VarianceScaling.__init__ (from tensorflow.python.ops.init_ops) with dtype is deprecated a
nd 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 /home/baozhigui/software/miniconda3/envs/svision/lib/python3.6/site-packages/tensorflow/python/ops/init_ops.py:1251: calling VarianceScaling.__init__ (from tensorflow.python.ops.init_ops) with dtype is deprecated a
nd 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 /home/baozhigui/software/miniconda3/envs/svision/lib/python3.6/site-packages/tensorflow/python/ops/init_ops.py:1251: calling VarianceScaling.__init__ (from tensorflow.python.ops.init_ops) with dtype is deprecated a
nd 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 /home/baozhigui/software/miniconda3/envs/svision/lib/python3.6/site-packages/tensorflow/python/ops/init_ops.py:1251: calling VarianceScaling.__init__ (from tensorflow.python.ops.init_ops) with dtype is deprecated a
nd 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 /home/baozhigui/software/miniconda3/envs/svision/lib/python3.6/site-packages/tensorflow/python/ops/init_ops.py:1251: calling VarianceScaling.__init__ (from tensorflow.python.ops.init_ops) with dtype is deprecated a
nd 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 /home/baozhigui/software/miniconda3/envs/svision/lib/python3.6/site-packages/tensorflow/python/ops/init_ops.py:1251: calling VarianceScaling.__init__ (from tensorflow.python.ops.init_ops) with dtype is deprecated a
nd 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 /home/baozhigui/software/miniconda3/envs/svision/lib/python3.6/site-packages/tensorflow/python/ops/init_ops.py:1251: calling VarianceScaling.__init__ (from tensorflow.python.ops.init_ops) with dtype is deprecated a
nd 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 /home/baozhigui/software/miniconda3/envs/svision/lib/python3.6/site-packages/tensorflow/python/ops/init_ops.py:1251: calling VarianceScaling.__init__ (from tensorflow.python.ops.init_ops) with dtype is deprecated a
nd will be removed in a future version.
Instructions for updating:
Call initializer instance with the dtype argument instead of passing it to the constructor
2022-06-30 01:57:28.101392: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA
2022-06-30 01:57:28.101412: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA
2022-06-30 01:57:28.101450: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA
2022-06-30 01:57:28.101547: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA
2022-06-30 01:57:28.101499: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA
2022-06-30 01:57:28.101613: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA
2022-06-30 01:57:28.101656: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA
2022-06-30 01:57:28.101579: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA
2022-06-30 01:57:28.101697: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA
2022-06-30 01:57:28.101724: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA
2022-06-30 01:57:29.567614: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2100000000 Hz
2022-06-30 01:57:29.568114: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2100000000 Hz
2022-06-30 01:57:29.568661: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2100000000 Hz
2022-06-30 01:57:29.569017: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2100000000 Hz
2022-06-30 01:57:29.569397: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2100000000 Hz
2022-06-30 01:57:29.569590: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2100000000 Hz
2022-06-30 01:57:29.569878: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2100000000 Hz
2022-06-30 01:57:29.569904: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2100000000 Hz
terminate called after throwing an instance of 'std::system_error'
terminate called after throwing an instance of 'std::system_error  what():  Resource temporarily unavailable
'
  what():  Resource temporarily unavailable
terminate called after throwing an instance of 'std::system_error'
terminate called after throwing an instance of 'std::system_error'
  what():  Resource temporarily unavailable
  what():  Resource temporarily unavailable
terminate called after throwing an instance of 'std::system_error'
  what():  Resource temporarily unavailable
terminate called after throwing an instance of 'std::system_error'
  what():  Resource temporarily unavailable
terminate called after throwing an instance of 'std::system_error'
terminate called after throwing an instance of 'std::system_error'
  what():  Resource temporarily unavailable
  what():  Resource temporarily unavailable
terminate called after throwing an instance of 'std::system_error'
  what():  Resource temporarily unavailable
terminate called after throwing an instance of 'std::system_error'
  what():  Resource temporarily unavailable
WARNING:tensorflow:From /home/baozhigui/software/miniconda3/envs/svision/lib/python3.6/site-packages/tensorflow/python/ops/init_ops.py:1251: calling VarianceScaling.__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 /home/baozhigui/software/miniconda3/envs/svision/lib/python3.6/site-packages/tensorflow/python/ops/init_ops.py:1251: calling VarianceScaling.__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
2022-06-30 01:57:33.143280: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA
2022-06-30 01:57:33.151285: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA
2022-06-30 01:57:33.163466: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2100000000 Hz
2022-06-30 01:57:33.186161: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2100000000 Hz
2022-06-30 01:57:33.186280: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x2b7230735c30 executing computations on platform Host. Devices:
2022-06-30 01:57:33.188934: I tensorflow/compiler/xla/service/service.cc:175]   StreamExecutor device (0): <undefined>, <undefined>
2022-06-30 01:57:33.202338: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x2b7230735c30 executing computations on platform Host. Devices:
2022-06-30 01:57:33.202400: I tensorflow/compiler/xla/service/service.cc:175]   StreamExecutor device (0): <undefined>, <undefined>
2022-06-30 01:57:34.768652: W tensorflow/compiler/jit/mark_for_compilation_pass.cc:1412] (One-time warning): Not using XLA:CPU for cluster because envvar TF_XLA_FLAGS=--tf_xla_cpu_global_jit was not set.  If you want XLA:CPU, either set that envvar, or use experimental_jit_scope to enable XLA:CPU.  To confirm that XLA is active, pass --vmodule=xla_compilation_cache=1 (as a proper command-line flag, not via TF_XLA_FLAGS) or set the envvar XLA_FLAGS=--xla_hlo_profile.
2022-06-30 01:57:34.768677: W tensorflow/compiler/jit/mark_for_compilation_pass.cc:1412] (One-time warning): Not using XLA:CPU for cluster because envvar TF_XLA_FLAGS=--tf_xla_cpu_global_jit was not set.  If you want XLA:CPU, either set that envvar, or use experimental_jit_scope to enable XLA:CPU.  To confirm that XLA is active, pass --vmodule=xla_compilation_cache=1 (as a proper command-line flag, not via TF_XLA_FLAGS) or set the envvar XLA_FLAGS=--xla_hlo_profile.
WARNING:tensorflow:From /home/baozhigui/software/miniconda3/envs/svision/lib/python3.6/site-packages/tensorflow/python/training/saver.py:1276: checkpoint_exists (from tensorflow.python.training.checkpoint_management) is deprecated and will be removed in a future version.
Instructions for updating:
Use standard file APIs to check for files with this prefix.
WARNING:tensorflow:From /home/baozhigui/software/miniconda3/envs/svision/lib/python3.6/site-packages/tensorflow/python/training/saver.py:1276: checkpoint_exists (from tensorflow.python.training.checkpoint_management) is deprecated and will be removed in a future version.
Instructions for updating:
Use standard file APIs to check for files with this prefix.
INFO:tensorflow:Restoring parameters from /public/agis/huangsanwen_group/baozhigui/software/SVision/SVision_CNN/svision-cnn-model.ckpt
INFO:tensorflow:Restoring parameters from /public/agis/huangsanwen_group/baozhigui/software/SVision/SVision_CNN/svision-cnn-model.ckpt
@jiadong324 jiadong324 added the enhancement New feature or request label Jun 30, 2022
@baozg baozg changed the title Adding checkpoint for step1 and step2 [enhancement] Adding checkpoint for step1 and step2 Jun 30, 2022
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