Urllib3 error

[groponp]

I'm getting following error: raise ReadTimeoutError(self._pool, None, "Read timed out.") urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. It's a error of my internet connection or a bug ? I hope a help.

[martin-steinegger]

Does this problem persist after reseting of Colab?

[groponp]

I'm running into linux system. usin following command:

colabfold_batch --amber --templates --num-recycle 3 --zip --msa-mode "mmseqs2_uniref_env" --num-relax 1 --pair-mode "unpaired_paired" alphafold/AQPs/PF3D7_0810400.fasta AQPs_models/

I have restart my computer and persist.

[groponp]

and when I running on google colab, getting it error:
2023-02-21 04:13:42,949 Running on GPU
2023-02-21 04:13:42,963 Found 7 citations for tools or databases
2023-02-21 04:13:42,965 Query 1/1: PF3D7_0810400.1-p1 (length 603)
2023-02-21 04:14:08,927 Sequence 0 found templates: ['3iyz_A', '6kxw_A', '4jc6_A', '3cn5_A', '2zz9_A', '2d57_A', '1j4n_A', '6qim_B', '3gd8_A', '3d9s_D', '3ne2_C', '5c5x_D', '2b6o_A', '1sor_A', '2b6p_A', '3m9i_A', '2f2b_A', '7nl4_A', '7cjs_A', '7cjs_D']
2023-02-21 04:14:09,052 Setting max_seq=364, max_extra_seq=1
2023-02-21 04:15:54,158 alphafold2_ptm_model_3_seed_000 recycle=0 pLDDT=44.8 pTM=0.394
2023-02-21 04:17:09,497 alphafold2_ptm_model_3_seed_000 recycle=1 pLDDT=51.1 pTM=0.521 tol=11.4
2023-02-21 04:18:24,752 alphafold2_ptm_model_3_seed_000 recycle=2 pLDDT=51.2 pTM=0.518 tol=5
2023-02-21 04:19:39,841 alphafold2_ptm_model_3_seed_000 recycle=3 pLDDT=51.3 pTM=0.517 tol=3.42
2023-02-21 04:19:39,843 alphafold2_ptm_model_3_seed_000 took 321.9s (3 recycles)
2023-02-21 04:20:55,275 alphafold2_ptm_model_4_seed_000 recycle=0 pLDDT=43.9 pTM=0.393
2023-02-21 04:22:10,598 alphafold2_ptm_model_4_seed_000 recycle=1 pLDDT=49.7 pTM=0.472 tol=14.4
2023-02-21 04:23:25,871 alphafold2_ptm_model_4_seed_000 recycle=2 pLDDT=50.1 pTM=0.476 tol=4.43
2023-02-21 04:24:41,271 alphafold2_ptm_model_4_seed_000 recycle=3 pLDDT=50.1 pTM=0.482 tol=3.05
2023-02-21 04:24:41,274 alphafold2_ptm_model_4_seed_000 took 300.9s (3 recycles)
2023-02-21 04:25:57,152 alphafold2_ptm_model_5_seed_000 recycle=0 pLDDT=48.8 pTM=0.471
2023-02-21 04:27:12,548 alphafold2_ptm_model_5_seed_000 recycle=1 pLDDT=49.6 pTM=0.511 tol=16.3
2023-02-21 04:28:27,862 alphafold2_ptm_model_5_seed_000 recycle=2 pLDDT=48.8 pTM=0.505 tol=9.96
2023-02-21 04:29:42,973 alphafold2_ptm_model_5_seed_000 recycle=3 pLDDT=50.6 pTM=0.529 tol=5.19
2023-02-21 04:29:42,975 alphafold2_ptm_model_5_seed_000 took 300.8s (3 recycles)

---------------------------------------------------------------------------
UnfilteredStackTrace                      Traceback (most recent call last)
[<ipython-input-16-bd0d6a7e06e7>](https://localhost:8080/#) in <module>
     18 queries, is_complex = get_queries(input_dir)
---> 19 run(
     20     queries=queries,

57 frames
UnfilteredStackTrace: KeyError: 'template_mask'

The stack trace below excludes JAX-internal frames.
The preceding is the original exception that occurred, unmodified.

--------------------

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

KeyError Traceback (most recent call last) /usr/local/lib/python3.8/dist-packages/alphafold/model/modules.py in call(self, query_embedding, template_batch, mask_2d, is_training) 2222 """ 2223 -> 2224 num_templates = template_batch['template_mask'].shape[0] 2225 num_channels = (self.config.template_pair_stack 2226 .triangle_attention_ending_node.value_dim)

KeyError: 'template_mask'

[sokrypton]

the last bug involving template_mask should now be fixed.

See: https://github.com/sokrypton/ColabFold/commit/8c745219964d6bfb878dd6fb53b5a2a05b009391

[groponp]

The fix here, also here urllib3 error "time out", or is a error on my internetconnection

[Fox4Fun31]

Hi, I am new to the whole topic of programming, and I have an error with a python script that uses urllib3. When I scrape something from a website, and that website goes down for a few seconds, the script crashes completely, is there anything I can do to make it try to reconnect more times when this happens?