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kishwarshafin avatar kishwarshafin commented on May 8, 2024

@gevro ,

Can you please confirm that you are not useing r0.2 models with r0.3 codebase? This looks like you are using an older model with newer release.

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gevro avatar gevro commented on May 8, 2024

I am using r0.3.1 docker and I downloaded model from the link in the quick start:
gsutil cp -r gs://brain-genomics-public/research/deepconsensus/models/v0.3/model_checkpoint/*

Is that not correct?

Thanks.

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kishwarshafin avatar kishwarshafin commented on May 8, 2024

@gevro ,

In that case, can you please put down the full command that you are running here? I just followed the https://github.com/google/deepconsensus/blob/r0.3/docs/quick_start.md to run everything on a VM and everything seems to work correctly.

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gevro avatar gevro commented on May 8, 2024

Sure, here is the command:

singularity run -W /data -B /scratch/projects/lab/bin/deepconsensus/model:/model -B `pwd` /scratch/bin/deepconsensus/deepconsensus_0.3.1.sif deepconsensus run --batch_size=1024 --batch_zmws=100 --cpus 8 --max_passes 100 --subreads_to_ccs=subreads_to_ccs.bam --ccs_bam=ccs.bam --checkpoint=/model/checkpoint --output=output.deepconsensus.fastq

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kishwarshafin avatar kishwarshafin commented on May 8, 2024

@gevro , I believe the download didn't happen correctly in this case. Can you please run the following commands and try one more time:

mkdir /scratch/projects/lab/bin/deepconsensus/model/v0.3_model
cd /scratch/projects/lab/bin/deepconsensus/model/v0.3_model
gsutil cp -r gs://brain-genomics-public/research/deepconsensus/models/v0.3/model_checkpoint/'*' .
ls -lha

And verify the output (file size) matches to this:

103M Aug  1 17:54 checkpoint.data-00000-of-00001
4.9K Aug  1 17:54 checkpoint.index
3.4K Aug  1 17:54 params.json

And then run:

singularity run -W /data -B /scratch/projects/lab/bin/deepconsensus/model/v0.3_model:/model -B `pwd` /scratch/bin/deepconsensus/deepconsensus_0.3.1.sif deepconsensus run --batch_size=1024 --batch_zmws=100 --cpus 8 --max_passes 100 --subreads_to_ccs=subreads_to_ccs.bam --ccs_bam=ccs.bam --checkpoint=/model/checkpoint --output=output.deepconsensus.fastq

This should work.

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gevro avatar gevro commented on May 8, 2024

However, I checked and that downloads the same files I already have. What else could be the issue?

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kishwarshafin avatar kishwarshafin commented on May 8, 2024

@gevro ,

did you make sure that the directory you downloaded to didn't contain v0.2 checkpoint from before? Can you please run the instructed commands as a sanity check that the download wasn't the issue? I get the same error as you when I run deepconsensus v0.3.1 with v0.2 models so I am suspecting that is the issue.

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gevro avatar gevro commented on May 8, 2024

I'm still getting the same error. Maybe your docker deepconsensus_0.3.1 is the problem and has the wrong version of deepconsensus packaged inside?

Can you double check using your docker?

If not, how do we fix this issue?

_________________________________________________________________
Traceback (most recent call last):
  File "/home/lab/.local/lib/python3.8/site-packages/tensorflow/python/training/saving/saveable_object_util.py", line 130, in restore
    assigned_variable = resource_variable_ops.shape_safe_assign_variable_handle(
  File "/home/lab/.local/lib/python3.8/site-packages/tensorflow/python/ops/resource_variable_ops.py", line 308, in shape_safe_assign_variable_handle
    shape.assert_is_compatible_with(value_tensor.shape)
  File "/home/lab/.local/lib/python3.8/site-packages/tensorflow/python/framework/tensor_shape.py", line 1291, in assert_is_compatible_with
    raise ValueError("Shapes %s and %s are incompatible" % (self, other))
ValueError: Shapes (2640, 280) and (560, 280) are incompatible

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/opt/conda/envs/bio/bin/deepconsensus", line 8, in <module>
    sys.exit(run())
  File "/opt/conda/envs/bio/lib/python3.8/site-packages/deepconsensus/cli.py", line 111, in run
    app.run(main, flags_parser=parse_flags)
  File "/share/apps/python/3.8.6/intel/lib/python3.8/site-packages/absl/app.py", line 312, in run
    _run_main(main, args)
  File "/share/apps/python/3.8.6/intel/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main
    sys.exit(main(argv))
  File "/opt/conda/envs/bio/lib/python3.8/site-packages/deepconsensus/cli.py", line 102, in main
    app.run(quick_inference.main, argv=passed)
  File "/share/apps/python/3.8.6/intel/lib/python3.8/site-packages/absl/app.py", line 312, in run
    _run_main(main, args)
  File "/share/apps/python/3.8.6/intel/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main
    sys.exit(main(argv))
  File "/opt/conda/envs/bio/lib/python3.8/site-packages/deepconsensus/inference/quick_inference.py", line 814, in main
    outcome_counter = run()
  File "/opt/conda/envs/bio/lib/python3.8/site-packages/deepconsensus/inference/quick_inference.py", line 734, in run
    loaded_model, model_params = initialize_model(
  File "/opt/conda/envs/bio/lib/python3.8/site-packages/deepconsensus/inference/quick_inference.py", line 476, in initialize_model
    checkpoint.restore(
  File "/home/lab/.local/lib/python3.8/site-packages/tensorflow/python/training/tracking/util.py", line 2537, in restore
    status = self.read(save_path, options=options)
  File "/home/lab/.local/lib/python3.8/site-packages/tensorflow/python/training/tracking/util.py", line 2417, in read
    result = self._saver.restore(save_path=save_path, options=options)
  File "/home/lab/.local/lib/python3.8/site-packages/tensorflow/python/training/tracking/util.py", line 1468, in restore
    base.CheckpointPosition(
  File "/home/lab/.local/lib/python3.8/site-packages/tensorflow/python/training/tracking/base.py", line 295, in restore
    restore_ops = trackable._restore_from_checkpoint_position(self)  # pylint: disable=protected-access
  File "/home/lab/.local/lib/python3.8/site-packages/tensorflow/python/training/tracking/base.py", line 1060, in _restore_from_checkpoint_position
    current_position.checkpoint.restore_saveables(tensor_saveables,
  File "/home/lab/.local/lib/python3.8/site-packages/tensorflow/python/training/tracking/util.py", line 349, in restore_saveables
    new_restore_ops = functional_saver.MultiDeviceSaver(
  File "/home/lab/.local/lib/python3.8/site-packages/tensorflow/python/training/saving/functional_saver.py", line 415, in restore
    restore_ops = restore_fn()
  File "/home/lab/.local/lib/python3.8/site-packages/tensorflow/python/training/saving/functional_saver.py", line 398, in restore_fn
    restore_ops.update(saver.restore(file_prefix, options))
  File "/home/lab/.local/lib/python3.8/site-packages/tensorflow/python/training/saving/functional_saver.py", line 112, in restore
    restore_ops[saveable.name] = saveable.restore(
  File "/home/lab/.local/lib/python3.8/site-packages/tensorflow/python/training/saving/saveable_object_util.py", line 133, in restore
    raise ValueError(
ValueError: Received incompatible tensor with shape (560, 280) when attempting to restore variable with shape (2640, 280) and name model/transformer_input_condenser/kernel/.ATTRIBUTES/VARIABLE_VALUE.
WARNING:tensorflow:Detecting that an object or model or tf.train.Checkpoint is being deleted with unrestored values. See the following logs for the specific values in question. To silence these warnings, use `status.expect_partial()`. See https://www.tensorflow.org/api_docs/python/tf/train/Checkpoint#restorefor details about the status object returned by the restore function.
W0802 21:18:21.240287 23396527953728 util.py:200] Detecting that an object or model or tf.train.Checkpoint is being deleted with unrestored values. See the following logs for the specific values in question. To silence these warnings, use `status.expect_partial()`. See https://www.tensorflow.org/api_docs/python/tf/train/Checkpoint#restorefor details about the status object returned by the restore function.
WARNING:tensorflow:Value in checkpoint could not be found in the restored object: (root).save_counter
W0802 21:18:21.240466 23396527953728 util.py:209] Value in checkpoint could not be found in the restored object: (root).save_counter
WARNING:tensorflow:Value in checkpoint could not be found in the restored object: (root).optimizer.iter
W0802 21:18:21.240509 23396527953728 util.py:209] Value in checkpoint could not be found in the restored object: (root).optimizer.iter

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pichuan avatar pichuan commented on May 8, 2024

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gevro avatar gevro commented on May 8, 2024

Ok thanks. Is there any possibility to train a model for higher max_passes?

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gevro avatar gevro commented on May 8, 2024

Also, now I'm getting a different error:

=================================================================
Total params: 8,942,667
Trainable params: 8,942,667
Non-trainable params: 0
_________________________________________________________________
I0802 23:05:13.125668 22923163895616 model_utils.py:231] Setting hidden size to transformer_input_size.
I0802 23:05:13.125833 22923163895616 quick_inference.py:484] Finished initialize_model.
I0802 23:05:13.126322 22923163895616 quick_inference.py:738] Model setup took 0.6180477142333984 seconds.
Traceback (most recent call last):
  File "/opt/conda/envs/bio/lib/python3.8/site-packages/deepconsensus/preprocess/utils.py", line 981, in proc_feeder
    ccs_bam_read = next(ccs_bam_h)
  File "pysam/libcalignmentfile.pyx", line 1874, in pysam.libcalignmentfile.AlignmentFile.__next__
StopIteration

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/opt/conda/envs/bio/bin/deepconsensus", line 8, in <module>
    sys.exit(run())
  File "/opt/conda/envs/bio/lib/python3.8/site-packages/deepconsensus/cli.py", line 111, in run
    app.run(main, flags_parser=parse_flags)
  File "/share/apps/python/3.8.6/intel/lib/python3.8/site-packages/absl/app.py", line 312, in run
    _run_main(main, args)
  File "/share/apps/python/3.8.6/intel/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main
    sys.exit(main(argv))
  File "/opt/conda/envs/bio/lib/python3.8/site-packages/deepconsensus/cli.py", line 102, in main
    app.run(quick_inference.main, argv=passed)
  File "/share/apps/python/3.8.6/intel/lib/python3.8/site-packages/absl/app.py", line 312, in run
    _run_main(main, args)
  File "/share/apps/python/3.8.6/intel/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main
    sys.exit(main(argv))
  File "/opt/conda/envs/bio/lib/python3.8/site-packages/deepconsensus/inference/quick_inference.py", line 814, in main
    outcome_counter = run()
  File "/opt/conda/envs/bio/lib/python3.8/site-packages/deepconsensus/inference/quick_inference.py", line 762, in run
    for zmw, subreads, dc_config in input_file_generator:
  File "/opt/conda/envs/bio/lib/python3.8/site-packages/deepconsensus/inference/quick_inference.py", line 428, in stream_bam
    for input_data in proc_feeder():
RuntimeError: generator raised StopIteration

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danielecook avatar danielecook commented on May 8, 2024

@gevro what does the distribution of the number of passes look like in your dataset?

We do not expect a large benefit from training a model for more passes. Quality goes up as the number of subread passes increases, and DeepConsensus will not be necessary as the sequence becomes more correct.

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gevro avatar gevro commented on May 8, 2024

Is it possible to connect offline via e-mail so I can explain better?

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AndrewCarroll avatar AndrewCarroll commented on May 8, 2024

Hi @gevro

In terms of talking about model training possibilities by email, can you send a message to [email protected]. I can loop in Dan and we can continue discussion from there.

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danielecook avatar danielecook commented on May 8, 2024

I believe we have resolved this issue. If there are any further questions please reach out.

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