sokrypton / sokrypton/ColabFold
No info in output.cvs LazyAF colab AlphaFold2-Multimer
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Description
Expected Behavior
An output.csv table with a list of each interaction
Current Behavior
outup.csv table with neither names of proteins or pTM/ipTM scores
Steps to Reproduce (for bugs)
input_dir: /content/drive/MyDrive/input
result_dir: /content/drive/MyDrive/input_fasta
input_file: protsequence.txt
protsequence.txt
bait_protein_sequence: MARSKTAQPKHSLRKIAVVVATAVSGMSVYAQAAVEPKEDTITVTAAPAPQESAWGPAAT IAARQSATGTKTDTPIQKVPQSISVVTAEEMALHQPKSVKEALSYTPGVSVGTRGASNTY DHLIIRGFAAEGQSQNNYLNGLKLQGNFYNDAVIDPYMLERAEIMRGPVSVLYGKSSPGG LLNMVSKRPTTEPLKEVQFKAGTDSLFQTGFDFSDSLDDDGVYSYRLTGLARSANAQQKG SEEQRYAIAPAFTWRPDDKTNFTFLSYFQNEPETGYYGWLPKEGTVEPLPNGKRLPTDFN EGAKNNTYSRNEKMVGYSFDHEFNDTFTVRQNLRFAENKTSQNSVYGYGVCSDPANAYSK QCAALAPADKGHYLARKYVVDDEKLQNFSVDTQLQSKFATGDIDHTLLTGVDFMRMRNDI NAWFGYDDSVPLLNLYNPVNTDFDFNAKDPANSGPYRILNKQKQTGVYVQDQAQWDKVLV TLGGRYDWADQESLNRVAGTTDKRDDKQFTWRGGVNYLFDNGVTPYFSYSESFEPSSQVG KDGNIFAPSKGKQYEVGVKYVPEDRPIVVTGAVYNLTKTNNLMADPEGSFFSVEGGEIRA RGVEIEAKAALSASVNVVGSYTYTDAEYTTDTTYKGNTPAQVPKHMASLWADYTFFDGPL SGLTLGTGGRYTGSSYGDPANSFKVGSYTVVDALVRYDLARVGMAGSNVALHVNNLFDRE YVASCFNTYGCFWGAERQVVATATFRF
bait_protein_name: FhuA
ColabFold Output (for bugs)
Files attached in zip format
drive-download-20240316T110814Z-001.zip
Context
I want to test if the multimer model (through colab LazyAF) is able to predict a known interaction between a membrane protein (FhuA) from E. coli and a receptor binding protein (RBP5_BPT5) from T5 phage.
I curate my fasta file to contain just 2 protein sequences (one is the receptor binding protein)
I run the 3 parts of the pipeline with no error.
The output of pipeline 3 is the output.cvs table containing no information of the PPI.
By checking the log file in the result folder I see the following issue in line 4: Could not generate input features AAS77195.1-FhuA_: Invalid character in the sequence:
Your Environment
I run the colab in google chrome Version 122.0.6261.129 (Official Build) (64-bit)
Device specifications:
Processor 11th Gen Intel(R) Core(TM) i5-11400H @ 2.70GHz 2.69 GHz
Installed RAM 16,0 GB (15,8 GB usable)
System type 64-bit operating system, x64-based processor
Windows 11 Home
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 with the LazyAF Colab notebook and the supplied protsequence.txt, then inspect the attached output archive and the result-folder log, especially line 4 reporting an invalid sequence character. Reproduce the run with the provided inputs; done means the pipeline completes without that feature-generation error and output.csv contains the protein names and pTM/ipTM scores.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100