sokrypton / sokrypton/ColabFold
Timeout while submitting to MSA server
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Description
Hello,
After executing the command colabfold_batch exper/fasta-res/G0_G0.fasta exper/pdbs --num-models 5, I encountered the following errors:
2024-05-06 15:47:16,903 Unable to initialize backend 'rocm': NOT_FOUND: Could not find registered platform with name: "rocm". Available platform names are: CUDA
2024-05-06 15:47:16,905 Unable to initialize backend 'tpu': INTERNAL: Failed to open libtpu.so: libtpu.so: cannot open shared object file: No such file or directory
2024-05-06 15:47:16,927 Running on GPU
2024-05-06 15:47:17,628 Found 5 citations for tools or databases
2024-05-06 15:47:17,628 Query 1/1: G0_G0 (length 1334)
2024-05-06 15:47:24,534 Timeout while submitting to MSA server. Retrying...
2024-05-06 15:47:30,564 Timeout while submitting to MSA server. Retrying...
**Our IP is 172.31.226.55. After trying the command curl https://api.colabfold.com/queue, I received the following error: curl: (35) OpenSSL SSL_connect: SSL_ERROR_SYSCALL in connection to api.colabfold.com:443.
Your Environment
colabfold 1.5.5
Looking forward to your reply. Thank you.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reviewing the reported colabfold_batch command and the MSA submission timeout, then test the reported endpoint with curl https://api.colabfold.com/queue. Done means identifying whether the failure is in ColabFold or the connection to the MSA server and recording a reproducible resolution.
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Assessment
- Domain
- bioinformatics, networking
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100