Please cite ColabFold: Making protein folding accessible to all. Nature Methods (2022) if you use these predictions.
/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).
  % datetime.datetime.utcnow().strftime('%Y-%m-%d'))
INFO:__main__:Starting prediction on 2026-05-01 UTC time
INFO:__main__:Installing ColabFold on Google Colab virtual machine.
Installing ColabFold
Using Tesla T4 graphics processor
Downloading alphafold2_ptm weights to .: 100%|██████████| 3.47G/3.47G [03:19<00:00, 18.6MB/s]
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RuntimeError                              Traceback (most recent call last)
/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)
   1293         import jax.tools.colab_tpu
-> 1294         jax.tools.colab_tpu.setup_tpu()
   1295         logger.info('Running on TPU')

14 frames
/usr/local/lib/python3.12/dist-packages/jax/tools/colab_tpu.py in setup_tpu(tpu_driver_version)
     19   """Raises an error. Do not use."""
---> 20   raise RuntimeError(
     21     "jax.tools.colab_tpu.setup_tpu() was required for older JAX versions"

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.

During handling of the above exception, another exception occurred:

ImportError                               Traceback (most recent call last)
/tmp/ipykernel_5099/2047926643.py in <cell line: 0>()
    335 remove_from_list(seq_list, 'prokaryote')  # Obsolete "prokaryote" flag
    336 
--> 337 run_prediction(seq_list, use_templates = use_templates, energy_minimize = not dont_minimize)

/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)
     73 
     74     from colabfold.batch import run
---> 75     run(
     76       queries=queries,
     77       result_dir='.',

/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)
   1302             use_gpu_relax = False
   1303         else:
-> 1304             import tensorflow as tf
   1305             tf.get_logger().setLevel(logging.ERROR)
   1306             logger.info('Running on GPU')

/usr/local/lib/python3.12/dist-packages/tensorflow/__init__.py in <module>
     53 from tensorflow._api.v2 import autograph
     54 from tensorflow._api.v2 import bitwise
---> 55 from tensorflow._api.v2 import compat
     56 from tensorflow._api.v2 import config
     57 from tensorflow._api.v2 import data

/usr/local/lib/python3.12/dist-packages/tensorflow/_api/v2/compat/__init__.py in <module>
      6 import sys as _sys
      7 
----> 8 from tensorflow._api.v2.compat import v1
      9 from tensorflow._api.v2.compat import v2
     10 from tensorflow.python.compat.compat import forward_compatibility_horizon # line: 125

/usr/local/lib/python3.12/dist-packages/tensorflow/_api/v2/compat/v1/__init__.py in <module>
     28 from tensorflow._api.v2.compat.v1 import autograph
     29 from tensorflow._api.v2.compat.v1 import bitwise
---> 30 from tensorflow._api.v2.compat.v1 import compat
     31 from tensorflow._api.v2.compat.v1 import config
     32 from tensorflow._api.v2.compat.v1 import data

/usr/local/lib/python3.12/dist-packages/tensorflow/_api/v2/compat/v1/compat/__init__.py in <module>
      6 import sys as _sys
      7 
----> 8 from tensorflow._api.v2.compat.v1.compat import v1
      9 from tensorflow._api.v2.compat.v1.compat import v2
     10 from tensorflow.python.compat.compat import forward_compatibility_horizon # line: 125

/usr/local/lib/python3.12/dist-packages/tensorflow/_api/v2/compat/v1/compat/v1/__init__.py in <module>
     45 from tensorflow._api.v2.compat.v1 import layers
     46 from tensorflow._api.v2.compat.v1 import linalg
---> 47 from tensorflow._api.v2.compat.v1 import lite
     48 from tensorflow._api.v2.compat.v1 import logging
     49 from tensorflow._api.v2.compat.v1 import lookup

/usr/local/lib/python3.12/dist-packages/tensorflow/_api/v2/compat/v1/lite/__init__.py in <module>
      7 
      8 from tensorflow._api.v2.compat.v1.lite import constants
----> 9 from tensorflow._api.v2.compat.v1.lite import experimental
     10 from tensorflow.lite.python.convert import OpsSet # line: 151
     11 from tensorflow.lite.python.convert import toco_convert # line: 929

/usr/local/lib/python3.12/dist-packages/tensorflow/_api/v2/compat/v1/lite/experimental/__init__.py in <module>
      6 import sys as _sys
      7 
----> 8 from tensorflow._api.v2.compat.v1.lite.experimental import authoring
      9 from tensorflow.lite.python.analyzer import ModelAnalyzer as Analyzer # line: 35
     10 from tensorflow.lite.python.interpreter import OpResolverType # line: 315

/usr/local/lib/python3.12/dist-packages/tensorflow/_api/v2/compat/v1/lite/experimental/authoring/__init__.py in <module>
      6 import sys as _sys
      7 
----> 8 from tensorflow.lite.python.authoring.authoring import compatible # line: 263
      9 
     10 from tensorflow.python.util import module_wrapper as _module_wrapper

/usr/local/lib/python3.12/dist-packages/tensorflow/lite/python/authoring/authoring.py in <module>
     40 from tensorflow.compiler.mlir.lite.metrics import converter_error_data_pb2
     41 # pylint: disable=g-import-not-at-top
---> 42 from tensorflow.lite.python import convert
     43 from tensorflow.lite.python import lite
     44 from tensorflow.python.util.tf_export import tf_export as _tf_export

/usr/local/lib/python3.12/dist-packages/tensorflow/lite/python/convert.py in <module>
     32 from tensorflow.lite.python.convert_phase import ConverterError
     33 from tensorflow.lite.python.convert_phase import SubComponent
---> 34 from tensorflow.lite.python.metrics.wrapper import metrics_wrapper as _metrics_wrapper
     35 from tensorflow.lite.tools import flatbuffer_utils
     36 from tensorflow.python.framework import dtypes

/usr/local/lib/python3.12/dist-packages/tensorflow/lite/python/metrics/wrapper/metrics_wrapper.py in <module>
     17 from tensorflow.compiler.mlir.lite.metrics import converter_error_data_pb2
     18 from tensorflow.compiler.mlir.lite.python import wrap_converter
---> 19 from tensorflow.lite.python.metrics._pywrap_tensorflow_lite_metrics_wrapper import MetricsWrapper  # pylint: disable=unused-import
     20 
     21 

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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