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

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First steps

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  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 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

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