| 1 | Please cite ColabFold: Making protein folding accessible to all. Nature Methods (2022) if you use these predictions.
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| 2 | /tmp/ipykernel_5099/2047926643.py:117: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).
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| 3 | % datetime.datetime.utcnow().strftime('%Y-%m-%d'))
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| 4 | INFO:__main__:Starting prediction on 2026-05-01 UTC time
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| 5 | INFO:__main__:Installing ColabFold on Google Colab virtual machine.
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| 6 | Installing ColabFold
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| 7 | Using Tesla T4 graphics processor
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| 8 | Downloading alphafold2_ptm weights to .: 100%|ââââââââââ| 3.47G/3.47G [03:19<00:00, 18.6MB/s]
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| 9 | ---------------------------------------------------------------------------
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| 10 | RuntimeError Traceback (most recent call last)
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| 11 | /usr/local/lib/python3.12/dist-packages/colabfold/batch.py in run(queries, result_dir, num_models, is_complex, num_recycles, recycle_early_stop_tolerance, model_order, num_ensemble, model_type, msa_mode, use_templates, custom_template_path, num_relax, relax_max_iterations, relax_tolerance, relax_stiffness, relax_max_outer_iterations, keep_existing_results, rank_by, pair_mode, pairing_strategy, data_dir, host_url, user_agent, random_seed, num_seeds, recompile_padding, zip_results, prediction_callback, save_single_representations, save_pair_representations, jobname_prefix, save_all, save_recycles, use_dropout, use_gpu_relax, stop_at_score, dpi, max_seq, max_extra_seq, pdb_hit_file, local_pdb_path, use_cluster_profile, feature_dict_callback, calc_extra_ptm, use_probs_extra, **kwargs)
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| 12 | 1293 import jax.tools.colab_tpu
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| 13 | -> 1294 jax.tools.colab_tpu.setup_tpu()
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| 14 | 1295 logger.info('Running on TPU')
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| 15 |
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| 16 | 14 frames
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| 17 | /usr/local/lib/python3.12/dist-packages/jax/tools/colab_tpu.py in setup_tpu(tpu_driver_version)
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| 18 | 19 """Raises an error. Do not use."""
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| 19 | ---> 20 raise RuntimeError(
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| 20 | 21 "jax.tools.colab_tpu.setup_tpu() was required for older JAX versions"
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| 21 |
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| 22 | RuntimeError: jax.tools.colab_tpu.setup_tpu() was required for older JAX versions running on older generations of TPUs, and should no longer be used.
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| 23 |
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| 24 | During handling of the above exception, another exception occurred:
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| 25 |
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| 26 | ImportError Traceback (most recent call last)
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| 27 | /tmp/ipykernel_5099/2047926643.py in <cell line: 0>()
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| 28 | 335 remove_from_list(seq_list, 'prokaryote') # Obsolete "prokaryote" flag
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| 29 | 336
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| 30 | --> 337 run_prediction(seq_list, use_templates = use_templates, energy_minimize = not dont_minimize)
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| 31 |
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| 32 | /tmp/ipykernel_5099/2047926643.py in run_prediction(sequences, job_name, msa_mode, pair_mode, use_templates, custom_template_path, energy_minimize, model_type, num_recycles, dpi, install_log)
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| 33 | 73
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| 34 | 74 from colabfold.batch import run
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| 35 | ---> 75 run(
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| 36 | 76 queries=queries,
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| 37 | 77 result_dir='.',
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| 38 |
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| 39 | /usr/local/lib/python3.12/dist-packages/colabfold/batch.py in run(queries, result_dir, num_models, is_complex, num_recycles, recycle_early_stop_tolerance, model_order, num_ensemble, model_type, msa_mode, use_templates, custom_template_path, num_relax, relax_max_iterations, relax_tolerance, relax_stiffness, relax_max_outer_iterations, keep_existing_results, rank_by, pair_mode, pairing_strategy, data_dir, host_url, user_agent, random_seed, num_seeds, recompile_padding, zip_results, prediction_callback, save_single_representations, save_pair_representations, jobname_prefix, save_all, save_recycles, use_dropout, use_gpu_relax, stop_at_score, dpi, max_seq, max_extra_seq, pdb_hit_file, local_pdb_path, use_cluster_profile, feature_dict_callback, calc_extra_ptm, use_probs_extra, **kwargs)
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| 40 | 1302 use_gpu_relax = False
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| 41 | 1303 else:
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| 42 | -> 1304 import tensorflow as tf
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| 43 | 1305 tf.get_logger().setLevel(logging.ERROR)
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| 44 | 1306 logger.info('Running on GPU')
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| 45 |
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| 46 | /usr/local/lib/python3.12/dist-packages/tensorflow/__init__.py in <module>
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| 47 | 53 from tensorflow._api.v2 import autograph
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| 48 | 54 from tensorflow._api.v2 import bitwise
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| 49 | ---> 55 from tensorflow._api.v2 import compat
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| 50 | 56 from tensorflow._api.v2 import config
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| 51 | 57 from tensorflow._api.v2 import data
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| 52 |
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| 53 | /usr/local/lib/python3.12/dist-packages/tensorflow/_api/v2/compat/__init__.py in <module>
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| 54 | 6 import sys as _sys
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| 55 | 7
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| 56 | ----> 8 from tensorflow._api.v2.compat import v1
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| 57 | 9 from tensorflow._api.v2.compat import v2
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| 58 | 10 from tensorflow.python.compat.compat import forward_compatibility_horizon # line: 125
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| 59 |
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| 60 | /usr/local/lib/python3.12/dist-packages/tensorflow/_api/v2/compat/v1/__init__.py in <module>
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| 61 | 28 from tensorflow._api.v2.compat.v1 import autograph
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| 62 | 29 from tensorflow._api.v2.compat.v1 import bitwise
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| 63 | ---> 30 from tensorflow._api.v2.compat.v1 import compat
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| 64 | 31 from tensorflow._api.v2.compat.v1 import config
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| 65 | 32 from tensorflow._api.v2.compat.v1 import data
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| 66 |
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| 67 | /usr/local/lib/python3.12/dist-packages/tensorflow/_api/v2/compat/v1/compat/__init__.py in <module>
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| 68 | 6 import sys as _sys
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| 69 | 7
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| 70 | ----> 8 from tensorflow._api.v2.compat.v1.compat import v1
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| 71 | 9 from tensorflow._api.v2.compat.v1.compat import v2
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| 72 | 10 from tensorflow.python.compat.compat import forward_compatibility_horizon # line: 125
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| 73 |
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| 74 | /usr/local/lib/python3.12/dist-packages/tensorflow/_api/v2/compat/v1/compat/v1/__init__.py in <module>
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| 75 | 45 from tensorflow._api.v2.compat.v1 import layers
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| 76 | 46 from tensorflow._api.v2.compat.v1 import linalg
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| 77 | ---> 47 from tensorflow._api.v2.compat.v1 import lite
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| 78 | 48 from tensorflow._api.v2.compat.v1 import logging
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| 79 | 49 from tensorflow._api.v2.compat.v1 import lookup
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| 80 |
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| 81 | /usr/local/lib/python3.12/dist-packages/tensorflow/_api/v2/compat/v1/lite/__init__.py in <module>
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| 82 | 7
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| 83 | 8 from tensorflow._api.v2.compat.v1.lite import constants
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| 84 | ----> 9 from tensorflow._api.v2.compat.v1.lite import experimental
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| 85 | 10 from tensorflow.lite.python.convert import OpsSet # line: 151
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| 86 | 11 from tensorflow.lite.python.convert import toco_convert # line: 929
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| 87 |
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| 88 | /usr/local/lib/python3.12/dist-packages/tensorflow/_api/v2/compat/v1/lite/experimental/__init__.py in <module>
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| 89 | 6 import sys as _sys
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| 90 | 7
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| 91 | ----> 8 from tensorflow._api.v2.compat.v1.lite.experimental import authoring
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| 92 | 9 from tensorflow.lite.python.analyzer import ModelAnalyzer as Analyzer # line: 35
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| 93 | 10 from tensorflow.lite.python.interpreter import OpResolverType # line: 315
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| 94 |
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| 95 | /usr/local/lib/python3.12/dist-packages/tensorflow/_api/v2/compat/v1/lite/experimental/authoring/__init__.py in <module>
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| 96 | 6 import sys as _sys
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| 97 | 7
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| 98 | ----> 8 from tensorflow.lite.python.authoring.authoring import compatible # line: 263
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| 99 | 9
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| 100 | 10 from tensorflow.python.util import module_wrapper as _module_wrapper
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| 101 |
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| 102 | /usr/local/lib/python3.12/dist-packages/tensorflow/lite/python/authoring/authoring.py in <module>
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| 103 | 40 from tensorflow.compiler.mlir.lite.metrics import converter_error_data_pb2
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| 104 | 41 # pylint: disable=g-import-not-at-top
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| 105 | ---> 42 from tensorflow.lite.python import convert
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| 106 | 43 from tensorflow.lite.python import lite
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| 107 | 44 from tensorflow.python.util.tf_export import tf_export as _tf_export
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| 108 |
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| 109 | /usr/local/lib/python3.12/dist-packages/tensorflow/lite/python/convert.py in <module>
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| 110 | 32 from tensorflow.lite.python.convert_phase import ConverterError
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| 111 | 33 from tensorflow.lite.python.convert_phase import SubComponent
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| 112 | ---> 34 from tensorflow.lite.python.metrics.wrapper import metrics_wrapper as _metrics_wrapper
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| 113 | 35 from tensorflow.lite.tools import flatbuffer_utils
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| 114 | 36 from tensorflow.python.framework import dtypes
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| 115 |
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| 116 | /usr/local/lib/python3.12/dist-packages/tensorflow/lite/python/metrics/wrapper/metrics_wrapper.py in <module>
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| 117 | 17 from tensorflow.compiler.mlir.lite.metrics import converter_error_data_pb2
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| 118 | 18 from tensorflow.compiler.mlir.lite.python import wrap_converter
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| 119 | ---> 19 from tensorflow.lite.python.metrics._pywrap_tensorflow_lite_metrics_wrapper import MetricsWrapper # pylint: disable=unused-import
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| 120 | 20
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| 121 | 21
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| 122 |
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| 123 | ImportError: /usr/local/lib/python3.12/dist-packages/tensorflow/lite/python/metrics/_pywrap_tensorflow_lite_metrics_wrapper.so: undefined symbol: Wrapped_PyInit__pywrap_tensorflow_lite_metrics_wrapper
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| 124 |
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| 125 | ---------------------------------------------------------------------------
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| 126 | NOTE: If your import is failing due to a missing package, you can
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| 127 | manually install dependencies using either !pip or !apt.
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| 128 |
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| 129 | To view examples of installing some common dependencies, click the
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| 130 | "Open Examples" button below.
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| 131 | ---------------------------------------------------------------------------
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