sokrypton / sokrypton/ColabFold
Both ColabFold notebook and localcolabfold cannot predict this sequence.
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Description
Expected Behavior
My sequence is VQTLDEFTIQQMRNFPNATGELSGLLRDIGLAAKRVNVEVNKAGLVDILGDAGSVNVQGEEVKKLDVYANDQFMGVLRHGISCAGIGSEELDDVVIFDDEISNNSKYVCLFDPLDGSANIDVNVSIGTIFSVFRRVTPIGQPATEADFLQAGIRQIAAGYVIYGSSTILVYATRRGVNGFTLDPSIGEWTLSHPDIKCPPTGKIYSVNHGNFFQYDQGVQDYITACQRKDKTNGGPYTQRYIGSMVSDMHRNLIKGGIFMYPGYTGKPGGKLRLMYECNPFAFILEVAGGKATDGKNRILDKVPGHIHDRTPFFAGSKEMMEELETYLPK, which is produced by gene (IMG ID: 3300044540|Ga0451702_0009729|CDS|Ga0451702_0009729_952_1944|+|952:1944) transcription.
Current Behavior
In localcolabfold, I got the followings. I had tested it for many times, and it was always sleeping and PENDING. I had asked it to run all night, but after 11 hours, it was still stuck on sleeping and PENDING.
2024-10-29 17:45:11,843 Query 15/50: aabzA (length 330)
2024-10-29 17:45:13,451 Sleeping for 9s. Reason: PENDING
2024-10-29 17:45:23,584 Sleeping for 6s. Reason: PENDING
2024-10-29 17:45:30,715 Sleeping for 7s. Reason: PENDING
2024-10-29 17:45:38,830 Sleeping for 5s. Reason: PENDING
... ...
2024-10-29 17:48:02,390 Sleeping for 7s. Reason: PENDING
2024-10-29 17:48:10,692 Sleeping for 6s. Reason: PENDING
2024-10-29 17:48:17,870 Sleeping for 8s. Reason: PENDING
2024-10-29 17:48:27,195 Sleeping for 10s. Reason: PENDING
2024-10-29 17:48:38,348 Sleeping for 6s. Reason: PENDING
2024-10-29 17:48:46,016 Sleeping for 5s. Reason: PENDING
2024-10-29 17:48:52,242 Sleeping for 6s. Reason: PENDING
2024-10-29 17:48:59,529 Sleeping for 10s. Reason: PENDING
... ...
2024-10-29 17:51:44,062 Sleeping for 5s. Reason: PENDING
2024-10-29 17:51:50,706 Sleeping for 5s. Reason: PENDING
2024-10-29 17:51:56,885 Sleeping for 8s. Reason: PENDING
2024-10-29 17:52:06,066 Sleeping for 10s. Reason: PENDING
... ...
2024-10-29 18:00:47,716 Sleeping for 9s. Reason: PENDING
2024-10-29 18:00:57,929 Sleeping for 7s. Reason: PENDING
2024-10-29 18:01:06,480 Sleeping for 6s. Reason: PENDING
2024-10-29 18:01:13,658 Sleeping for 6s. Reason: PENDING
2024-10-29 18:01:20,780 Sleeping for 10s. Reason: PENDING
2024-10-29 18:01:32,096 Sleeping for 6s. Reason: PENDING
2024-10-29 18:01:39,422 Sleeping for 8s. Reason: PENDING
... ....
2024-10-29 18:05:16,270 Sleeping for 6s. Reason: PENDING
2024-10-29 18:05:23,511 Sleeping for 9s. Reason: PENDING
2024-10-29 18:05:33,636 Sleeping for 7s. Reason: PENDING
2024-10-29 18:05:41,849 Sleeping for 10s. Reason: PENDING
2024-10-29 18:05:53,029 Sleeping for 7s. Reason: PENDING
2024-10-29 18:06:01,183 Sleeping for 9s. Reason: PENDING
PENDING: 0%| | 0/150 [elapsed: 20:49 remaining: ?]
Then, I changed to use ColabFold notebook, but I met the same issue.
Steps to Reproduce (for bugs)
Please make sure to reproduce the issue after a "Factory Reset" in Colab.
If running locally ypdate you local installation colabfold_batch to the newest version.
Please provide your input if you can share it.
ColabFold Output (for bugs)
Please make sure to also post the complete ColabFold output. You can use gist.github.com for large output.
Context
Providing context helps us come up with a solution and improve our documentation for the future.
Your Environment
Include as many relevant details about the environment you experienced the bug in.
- Git commit used
- If you run it on a local system. Please add the server specifications
- Operating system and version:
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 reproducing the sequence prediction in the ColabFold notebook after a Factory Reset, then update the localcolabfold installation and compare its complete output. Check the reported PENDING behavior alongside the requested environment details and server specifications. Done means identifying why this input remains pending and documenting or fixing a reproducible cause.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100