No bed file

[masterzhen119]

I cut part of the renference genome and try to run the algorithm. The code report nothing. And I attach the file
data_0_reads_selected_bam.bam.sorted.zip.
Besides the error is:
WARNING:tensorflow:From /home/project11/software/anaconda3/envs/svisionenv/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
2023-06-20 15:48:32.545879: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2023-06-20 15:48:32.553149: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 3391985000 Hz
2023-06-20 15:48:32.556042: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x55f8b16fcf20 executing computations on platform Host. Devices:
2023-06-20 15:48:32.556077: I tensorflow/compiler/xla/service/service.cc:175] StreamExecutor device (0): ,
2023-06-20 15:48:32.605179: 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/project11/software/anaconda3/envs/svisionenv/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 /scratch/project11/SVision/Model/svision-cnn-model.ckpt
Empty output in the score file!!! Program exit

Best

Zhen

[jiadong324]

I looked at the IGV, it seems like that there are no breakpoints in your alignments. If there are aberrant alignments, SVision won't find any SV signatures, so that you will not find the BED file that saves those aberrant alignments.