sokrypton / sokrypton/ColabFold

Batch mode (skipping all sequences) I switched to older 1.2 and 1.2 works

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Description

I put ~200 .fasta sequences in a google drive folder

Expected Behavior

Last time I used it, it generate 200 AF2 PDB into the same folder

Current Behavior

It skipped all sequences, and seem to have problem reading the file names.
2022-01-18 00:15:22,962 non-fasta/a3m file in input directory: /content/drive/MyDrive/mt1/log.txt
2022-01-18 00:15:22,971 Running colabfold 1.2.0 (079ae0b32f6609a545b43803579ca111184e207d)
2022-01-18 00:15:22,979 Found 5 citations for tools or databases
2022-01-18 00:15:29,698 Query 1/202: _ (length 190)
COMPLETE: 100%|██████████| 150/150 [elapsed: 00:01 remaining: 00:00]
2022-01-18 00:15:31,772 Running model_3
2022-01-18 00:19:46,000 model_3 took 249.9s (3 recycles) with pLDDT 95.4
2022-01-18 00:19:47,558 reranking models based on average plddt
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It output one PDB, without the name I have in the fasta files
__unrelaxed_rank_1_model_3.pdb

My directory looks like this
image

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

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the colabfold_batch entry point and the batch input/output handling described by the log; compare how FASTA filenames become query names and how existing outputs are detected. Reproduce the issue with the provided Google Drive layout and verify that each sequence produces a correctly named PDB without being incorrectly reported as already done.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook
Domain
bioinformatics, machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
20/100

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