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sokrypton / ColabFold

Making Protein folding accessible to all!
MIT License
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Timeout while submitting to MSA server. Retrying... #495

Closed shhashem closed 7 months ago

shhashem commented 1 year ago

Expected Behavior

MSA server returning alignments

Current Behavior

Timeout while submitting to MSA server. Retrying...

Steps to Reproduce (for bugs)

colabfold_batch complex.csv COMPLEX --num-seeds 20 --num-recycle 2 --msa-mode mmseqs2_uniref_env --model-type alphafold2_multimer_v3 --rank multimer --pair-mode unpaired_paired --num-models 5 --use-dropout --save-recycles --amber --use-gpu-relax

ColabFold Output (for bugs)

2023-08-03 10:06:45,582 Running on GPU 2023-08-03 10:06:47,101 Found 5 citations for tools or databases 2023-08-03 10:06:47,102 Query 1/1: Complex (length 520) 2023-08-03 10:06:53,163 Timeout while submitting to MSA server. Retrying... 2023-08-03 10:06:59,205 Timeout while submitting to MSA server. Retrying...

Context

I am experiencing a problem with the generation of MSA. When running ColabFold, I get "Timeout while submitting to MSA server. Retrying..." in the logfile. Could you please assist in that? Thanks

Your Environment

Newest local ColabFold version: 1.5.2

milot-mirdita commented 1 year ago

I don't see any issues currently. Could you send me the IP from which you are submitting request? If you don't want to share your IP publicly, you can email me at milot at mirdita dot de.

shhashem commented 1 year ago

I have run a job and it works now.

Thanks!

jiejiangtao commented 7 months ago

I have run a job and it works now.

Thanks! Hello, I also met this problem, how did you solve it.

milot-mirdita commented 7 months ago

Please open a new GitHub issue with as much detail as possible (the full error message, etc.)