danielecook
commented
9 months ago The error reported in the docx file is:
I1219 05:41:37.963743 139694699493120 call_variants.py:338] Shape of input examples: [100, 221, 9]
2023-12-19 05:41:37.985946: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN)to use the following CPU instructions in performance-critical operations: AVX2 AVX512F FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-12-19 05:41:38.002687: I tensorflow/core/platform/profile_utils/cpu_utils.cc:104] CPU Frequency: 2100000000 Hz
2023-12-19 05:41:38.008172: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x5c08e10 initialized for platform Host (this does not guarantee that XLA will be used). Devices:
2023-12-19 05:41:38.008269: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version
2023-12-19 05:41:38.008459: I tensorflow/core/common_runtime/process_util.cc:146] Creating new thread pool with default inter op setting: 2. Tune using inter_op_parallelism_threads for best performance.
WARNING:tensorflow:Using temporary folder as model directory: /tmp/tmpz9j4xfvf
W1219 05:41:38.122338 139694699493120 estimator.py:1844] Using temporary folder as model directory: /tmp/tmpz9j4xfvf
INFO:tensorflow:Using config: {'_model_dir': '/tmp/tmpz9j4xfvf', '_tf_random_seed': None, '_save_summary_steps': 100, '_save_checkpoints_steps': None, '_save_checkpoints_secs': 600, '_session_config': , '_keep_checkpoint_max': 100000, '_keep_checkpoint_every_n_hours': 10000, '_log_step_count_steps': 100, '_train_distribute': None, '_device_fn': None, '_protocol': None, '_eval_distribute': None, '_experimental_distribute': None, '_experimental_max_worker_delay_secs': None, '_session_creation_timeout_secs': 7200, '_service': None, '_cluster_spec': ClusterSpec({}), '_task_type': 'worker', '_task_id': 0, '_global_id_in_cluster': 0, '_master': '', '_evaluation_master': '', '_is_chief': True, '_num_ps_replicas': 0, '_num_worker_replicas': 1}
I1219 05:41:38.123045 139694699493120 estimator.py:191] Using config: {'_model_dir': '/tmp/tmpz9j4xfvf', '_tf_random_seed': None, '_save_summary_steps': 100, '_save_checkpoints_steps': None, '_save_checkpoints_secs': 600, '_session_config': , '_keep_checkpoint_max': 100000, '_keep_checkpoint_every_n_hours': 10000, '_log_step_count_steps': 100, '_train_distribute': None, '_device_fn': None, '_protocol': None, '_eval_distribute': None, '_experimental_distribute': None, '_experimental_max_worker_delay_secs': None, '_session_creation_timeout_secs': 7200, '_service': None, '_cluster_spec': ClusterSpec({}), '_task_type': 'worker', '_task_id': 0, '_global_id_in_cluster': 0, '_master': '', '_evaluation_master': '', '_is_chief': True, '_num_ps_replicas': 0, '_num_worker_replicas': 1}
I1219 05:41:38.123484 139694699493120 call_variants.py:435] Writing calls to /output/intermediate_results_dir/call_variants_output.tfrecord.gz
WARNING:tensorflow:From /tmp/Bazel.runfiles_8s8eyzhg/runfiles/com_google_deepvariant/deepvariant/data_providers.py:375: parallel_interleave (from tensorflow.python.data.experimental.ops.interleave_ops) is deprecated and will be removed in a future version.
Instructions for updating:
Use `tf.data.Dataset.interleave(map_func, cycle_length, block_length, num_parallel_calls=tf.data.experimental.AUTOTUNE)` instead. If sloppy execution is desired, use `tf.data.Options.experimental_deterministic`.
W1219 05:41:38.154152 139694699493120 deprecation.py:323] From /tmp/Bazel.runfiles_8s8eyzhg/runfiles/com_google_deepvariant/deepvariant/data_providers.py:375: parallel_interleave (from tensorflow.python.data.experimental.ops.interleave_ops) is deprecated and will be removed in a future version.
Instructions for updating:
Use `tf.data.Dataset.interleave(map_func, cycle_length, block_length, num_parallel_calls=tf.data.experimental.AUTOTUNE)` instead. If sloppy execution is desired, use `tf.data.Options.experimental_deterministic`.
WARNING:tensorflow:From /tmp/Bazel.runfiles_8s8eyzhg/runfiles/com_google_deepvariant/deepvariant/data_providers.py:381: map_and_batch (from tensorflow.python.data.experimental.ops.batching) is deprecated and will be removed in a future version.
Instructions for updating:
Use `tf.data.Dataset.map(map_func, num_parallel_calls)` followed by `tf.data.Dataset.batch(batch_size, drop_remainder)`. Static tf.data optimizations will take care of using the fused implementation.
W1219 05:41:38.273121 139694699493120 deprecation.py:323] From /tmp/Bazel.runfiles_8s8eyzhg/runfiles/com_google_deepvariant/deepvariant/data_providers.py:381: map_and_batch (from tensorflow.python.data.experimental.ops.batching) is deprecated and will be removed in a future version.
Instructions for updating:
Use `tf.data.Dataset.map(map_func, num_parallel_calls)` followed by `tf.data.Dataset.batch(batch_size, drop_remainder)`. Static tf.data optimizations will take care of using the fused implementation.
INFO:tensorflow:Calling model_fn.
I1219 05:41:38.770528 139694699493120 estimator.py:1162] Calling model_fn.
WARNING:tensorflow:From /usr/local/lib/python3.6/dist-packages/tf_slim/layers/layers.py:1089: Layer.apply (from tensorflow.python.keras.engine.base_layer_v1) is deprecated and will be removed in a future version.
Instructions for updating:
Please use `layer.__call__` method instead.
W1219 05:41:38.779899 139694699493120 deprecation.py:323] From /usr/local/lib/python3.6/dist-packages/tf_slim/layers/layers.py:1089: Layer.apply (from tensorflow.python.keras.engine.base_layer_v1) is deprecated and will be removed in a future version.
Instructions for updating:
Please use `layer.__call__` method instead.
INFO:tensorflow:Done calling model_fn.
I1219 05:41:46.711198 139694699493120 estimator.py:1164] Done calling model_fn.
INFO:tensorflow:Graph was finalized.
I1219 05:41:48.157609 139694699493120 monitored_session.py:246] Graph was finalized.
INFO:tensorflow:Restoring parameters from /opt/models/pacbio/model.ckpt
I1219 05:41:48.159860 139694699493120 saver.py:1293] Restoring parameters from /opt/models/pacbio/model.ckpt
2023-12-19 05:41:48.711875: W tensorflow/core/framework/op_kernel.cc:1767] OP_REQUIRES failed at save_restore_v2_ops.cc:184 : Not found: /opt/models/pacbio/model.ckpt.data-00000-of-00001; No such file or directory
Traceback (most recent call last):
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/client/session.py", line 1365, in _do_call
return fn(*args)
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/client/session.py", line 1350, in _run_fn
target_list, run_metadata)
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/client/session.py", line 1443, in _call_tf_sessionrun
run_metadata)
tensorflow.python.framework.errors_impl.NotFoundError: /opt/models/pacbio/model.ckpt.data-00000-of-00001; No such file or directory
[[{{node save_1/RestoreV2}}]]
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/training/saver.py", line 1299, in restore
{self.saver_def.filename_tensor_name: save_path})
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/client/session.py", line 958, in run
run_metadata_ptr)
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/client/session.py", line 1181, in _run
feed_dict_tensor, options, run_metadata)
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/client/session.py", line 1359, in _do_run
run_metadata)
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/client/session.py", line 1384, in _do_call
raise type(e)(node_def, op, message)
tensorflow.python.framework.errors_impl.NotFoundError: /opt/models/pacbio/model.ckpt.data-00000-of-00001; No such file or directory
[[node save_1/RestoreV2 (defined at usr/local/lib/python3.6/dist-packages/tensorflow_estimator/python/estimator/estimator.py:629) ]]
Original stack trace for 'save_1/RestoreV2':
File "tmp/Bazel.runfiles_8s8eyzhg/runfiles/com_google_deepvariant/deepvariant/call_variants.py", line 502, in <module>
tf.compat.v1.app.run()
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/platform/app.py", line 40, in run
_run(main=main, argv=argv, flags_parser=_parse_flags_tolerate_undef)
File "tmp/Bazel.runfiles_8s8eyzhg/runfiles/absl_py/absl/app.py", line 299, in run
_run_main(main, args)
File "tmp/Bazel.runfiles_8s8eyzhg/runfiles/absl_py/absl/app.py", line 250, in _run_main
sys.exit(main(argv))
File "tmp/Bazel.runfiles_8s8eyzhg/runfiles/com_google_deepvariant/deepvariant/call_variants.py", line 492, in main
use_tpu=FLAGS.use_tpu,
File "tmp/Bazel.runfiles_8s8eyzhg/runfiles/com_google_deepvariant/deepvariant/call_variants.py", line 442, in call_variants
prediction = next(predictions)
File "usr/local/lib/python3.6/dist-packages/tensorflow_estimator/python/estimator/estimator.py", line 629, in predict
hooks=all_hooks) as mon_sess:
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/monitored_session.py", line 1038, in __init__
stop_grace_period_secs=stop_grace_period_secs)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/monitored_session.py", line 749, in __init__
self._sess = _RecoverableSession(self._coordinated_creator)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/monitored_session.py", line 1231, in __init__
_WrappedSession.__init__(self, self._create_session())
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/monitored_session.py", line 1236, in _create_session
return self._sess_creator.create_session()
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/monitored_session.py", line 902, in create_session
self.tf_sess = self._session_creator.create_session()
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/monitored_session.py", line 660, in create_session
self._scaffold.finalize()
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/monitored_session.py", line 235, in finalize
self._saver = training_saver._get_saver_or_default() # pylint: disable=protected-access
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/saver.py", line 607, in _get_saver_or_default
saver = Saver(sharded=True, allow_empty=True)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/saver.py", line 836, in __init__
self.build()
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/saver.py", line 848, in build
self._build(self._filename, build_save=True, build_restore=True)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/saver.py", line 886, in _build
build_restore=build_restore)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/saver.py", line 510, in _build_internal
restore_sequentially, reshape)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/saver.py", line 389, in _AddShardedRestoreOps
name="restore_shard"))
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/saver.py", line 336, in _AddRestoreOps
restore_sequentially)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/saver.py", line 583, in bulk_restore
return io_ops.restore_v2(filename_tensor, names, slices, dtypes)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/ops/gen_io_ops.py", line 1524, in restore_v2
name=name)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/op_def_library.py", line 744, in _apply_op_helper
attrs=attr_protos, op_def=op_def)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/ops.py", line 3485, in _create_op_internal
op_def=op_def)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/ops.py", line 1949, in __init__
self._traceback = tf_stack.extract_stack()
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/training/py_checkpoint_reader.py", line 70, in get_tensor
self, compat.as_bytes(tensor_str))
RuntimeError: Key _CHECKPOINTABLE_OBJECT_GRAPH not found in checkpoint
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/training/saver.py", line 1309, in restore
names_to_keys = object_graph_key_mapping(save_path)
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/training/saver.py", line 1627, in object_graph_key_mapping
object_graph_string = reader.get_tensor(trackable.OBJECT_GRAPH_PROTO_KEY)
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/training/py_checkpoint_reader.py", line 74, in get_tensor
error_translator(e)
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/training/py_checkpoint_reader.py", line 35, in error_translator
raise errors_impl.NotFoundError(None, None, error_message)
tensorflow.python.framework.errors_impl.NotFoundError: Key _CHECKPOINTABLE_OBJECT_GRAPH not found in checkpoint
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/tmp/Bazel.runfiles_8s8eyzhg/runfiles/com_google_deepvariant/deepvariant/call_variants.py", line 502, in <module>
tf.compat.v1.app.run()
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/platform/app.py", line 40, in run
_run(main=main, argv=argv, flags_parser=_parse_flags_tolerate_undef)
File "/tmp/Bazel.runfiles_8s8eyzhg/runfiles/absl_py/absl/app.py", line 299, in run
_run_main(main, args)
File "/tmp/Bazel.runfiles_8s8eyzhg/runfiles/absl_py/absl/app.py", line 250, in _run_main
sys.exit(main(argv))
File "/tmp/Bazel.runfiles_8s8eyzhg/runfiles/com_google_deepvariant/deepvariant/call_variants.py", line 492, in main
use_tpu=FLAGS.use_tpu,
File "/tmp/Bazel.runfiles_8s8eyzhg/runfiles/com_google_deepvariant/deepvariant/call_variants.py", line 442, in call_variants
prediction = next(predictions)
File "/usr/local/lib/python3.6/dist-packages/tensorflow_estimator/python/estimator/estimator.py", line 629, in predict
hooks=all_hooks) as mon_sess:
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/training/monitored_session.py", line 1038, in __init__
stop_grace_period_secs=stop_grace_period_secs)
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/training/monitored_session.py", line 749, in __init__
self._sess = _RecoverableSession(self._coordinated_creator)
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/training/monitored_session.py", line 1231, in __init__
_WrappedSession.__init__(self, self._create_session())
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/training/monitored_session.py", line 1236, in _create_session
return self._sess_creator.create_session()
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/training/monitored_session.py", line 902, in create_session
self.tf_sess = self._session_creator.create_session()
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/training/monitored_session.py", line 669, in create_session
init_fn=self._scaffold.init_fn)
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/training/session_manager.py", line 295, in prepare_session
config=config)
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/training/session_manager.py", line 209, in _restore_checkpoint
saver.restore(sess, checkpoint_filename_with_path)
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/training/saver.py", line 1315, in restore
err, "a Variable name or other graph key that is missing")
tensorflow.python.framework.errors_impl.NotFoundError: Restoring from checkpoint failed. This is most likely due to a Variable name or other graph key that is missing from the checkpoint. Please ensure that you have not altered the graph expected based on the checkpoint. Original error:
/opt/models/pacbio/model.ckpt.data-00000-of-00001; No such file or directory
[[node save_1/RestoreV2 (defined at usr/local/lib/python3.6/dist-packages/tensorflow_estimator/python/estimator/estimator.py:629) ]]
Original stack trace for 'save_1/RestoreV2':
File "tmp/Bazel.runfiles_8s8eyzhg/runfiles/com_google_deepvariant/deepvariant/call_variants.py", line 502, in <module>
tf.compat.v1.app.run()
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/platform/app.py", line 40, in run
_run(main=main, argv=argv, flags_parser=_parse_flags_tolerate_undef)
File "tmp/Bazel.runfiles_8s8eyzhg/runfiles/absl_py/absl/app.py", line 299, in run
_run_main(main, args)
File "tmp/Bazel.runfiles_8s8eyzhg/runfiles/absl_py/absl/app.py", line 250, in _run_main
sys.exit(main(argv))
File "tmp/Bazel.runfiles_8s8eyzhg/runfiles/com_google_deepvariant/deepvariant/call_variants.py", line 492, in main
use_tpu=FLAGS.use_tpu,
File "tmp/Bazel.runfiles_8s8eyzhg/runfiles/com_google_deepvariant/deepvariant/call_variants.py", line 442, in call_variants
prediction = next(predictions)
File "usr/local/lib/python3.6/dist-packages/tensorflow_estimator/python/estimator/estimator.py", line 629, in predict
hooks=all_hooks) as mon_sess:
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/monitored_session.py", line 1038, in __init__
stop_grace_period_secs=stop_grace_period_secs)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/monitored_session.py", line 749, in __init__
self._sess = _RecoverableSession(self._coordinated_creator)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/monitored_session.py", line 1231, in __init__
_WrappedSession.__init__(self, self._create_session())
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/monitored_session.py", line 1236, in _create_session
return self._sess_creator.create_session()
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/monitored_session.py", line 902, in create_session
self.tf_sess = self._session_creator.create_session()
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/monitored_session.py", line 660, in create_session
self._scaffold.finalize()
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/monitored_session.py", line 235, in finalize
self._saver = training_saver._get_saver_or_default() # pylint: disable=protected-access
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/saver.py", line 607, in _get_saver_or_default
saver = Saver(sharded=True, allow_empty=True)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/saver.py", line 836, in __init__
self.build()
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/saver.py", line 848, in build
self._build(self._filename, build_save=True, build_restore=True)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/saver.py", line 886, in _build
build_restore=build_restore)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/saver.py", line 510, in _build_internal
restore_sequentially, reshape)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/saver.py", line 389, in _AddShardedRestoreOps
name="restore_shard"))
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/saver.py", line 336, in _AddRestoreOps
restore_sequentially)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/training/saver.py", line 583, in bulk_restore
return io_ops.restore_v2(filename_tensor, names, slices, dtypes)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/ops/gen_io_ops.py", line 1524, in restore_v2
name=name)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/op_def_library.py", line 744, in _apply_op_helper
attrs=attr_protos, op_def=op_def)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/ops.py", line 3485, in _create_op_internal
op_def=op_def)
File "usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/ops.py", line 1949, in __init__
self._traceback = tf_stack.extract_stack()
real 0m19.667s
user 0m15.445s
sys 0m3.603s
I1219 05:41:49.700348 140338112591616 run_deepvariant.py:416] None
Traceback (most recent call last):
File "/opt/deepvariant/bin/run_deepvariant.py", line 421, in <module>
app.run(main)
File "/usr/local/lib/python3.6/dist-packages/absl/app.py", line 299, in run
_run_main(main, args)
File "/usr/local/lib/python3.6/dist-packages/absl/app.py", line 250, in _run_main
sys.exit(main(argv))
File "/opt/deepvariant/bin/run_deepvariant.py", line 414, in main
subprocess.check_call(command, shell=True, executable='/bin/bash')
File "/usr/lib/python3.6/subprocess.py", line 311, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '( time /opt/deepvariant/bin/call_variants --outfile "/output/intermediate_results_dir/call_variants_output.tfrecord.gz" --examples "/output/intermediate_results_dir/make_examples.tfrecord@30.gz" --checkpoint "/opt/models/pacbio/model.ckpt" )' returned non-zero exit status 1.The error seems to suggest that the model file (/opt/models/pacbio/model.ckpt.data-00000-of-00001) does not exist.
Can you try running the following command:
BIN_VERSION="1.1.0"
docker run -it google/deepvariant:"${BIN_VERSION}" /bin/bash
ls /opt/models/pacbio/model.ckpt.data-00000-of-00001You should see the following output:
└──╼ docker run -it google/deepvariant:1.1.0 /bin/bash
$root@df876e3a15f7:/opt/deepvariant# ls /opt/models/pacbio/
model.ckpt.data-00000-of-00001 model.ckpt.index model.ckpt.meta
$root@df876e3a15f7:/opt/deepvariant# ls /opt/models/pacbio/model.ckpt.data-00000-of-00001
/opt/models/pacbio/model.ckpt.data-00000-of-00001
hcsun1
pichuan
Hello,
Thank you very much for providing the software. However, when I run deepvariant v1.1.0, I encounter the following file error. I did not encounter this error before. I hope you can help me solve this problem. Thank you very much for your assistance.
Below is my commond:
BIN_VERSION="1.1.0" INPUT_DIR="/data/lilab/hli1/Workspace/DATA/run_out_data/sorted_BAM/vs_F/6_2_vsF"
DATA_HTTP_DIR="https://storage.googleapis.com/deepvariant/quickstart-testdata"
OUTPUT_DIR="${PWD}/run_DeepVariant_6-20231219" mkdir -p "${OUTPUT_DIR}"
docker run \ -v "${INPUT_DIR}":"/input" \ -v "${OUTPUT_DIR}":"/output" \ google/deepvariant:"${BIN_VERSION}" \ /opt/deepvariant/bin/run_deepvariant \ --model_type=PACBIO \ --ref=/input/F_unphased.Chr.v2.fa \ --reads=/input/6ccs_2_vsF.sorted.bam \ --output_vcf=/output/output.vcf.gz \ --output_gvcf=/output/output.g.vcf.gz \ --intermediate_results_dir /output/intermediate_results_dir \ --num_shards=30 DeepVariant-v1.1.0.docx