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fold_analysis_latest.sif generation scores problem #480

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Qrouger opened this issue Jan 20, 2025 · 4 comments
Open

fold_analysis_latest.sif generation scores problem #480

Qrouger opened this issue Jan 20, 2025 · 4 comments
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@Qrouger
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Qrouger commented Jan 20, 2025

Hi, the latest version of the Singularity image for generate scores don't calculate pi_score for me.

predictions_with_good_interpae.csv

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@DimaMolod
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yes, this is because we removed ccp4 from the image. Please refer to #472

@DimaMolod DimaMolod added the duplicate This issue or pull request already exists label Jan 20, 2025
@Qrouger Qrouger closed this as completed Jan 20, 2025
@Qrouger
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Qrouger commented Jan 23, 2025

I'm sorry but I cannot generate the pi_score by following the image build with ccp4. It's maybe cause by the ccp4 version (v9.0.005) ?

@DimaMolod
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I am sorry to hear that. Yes, it could be because of incompatible ccp4 version, could you try to downgrade ccp4? Can you also provide log files with exact exceptions? If they are not informative, there is a trick you could try:
run your singularity image interactively with this command:
singularity shell /path/to/container.sif
...and try to run pi score script from within the container using these scripts:
https://github.com/KosinskiLab/AlphaPulldown/blob/main/alphapulldown/analysis_pipeline/run_pi_score.sh
https://github.com/KosinskiLab/AlphaPulldown/blob/main/alphapulldown/analysis_pipeline/run_get_good_pae.sh
the chances are that this way you will be able to get a more comprehensive error message.

@DimaMolod DimaMolod reopened this Jan 24, 2025
@Qrouger
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Qrouger commented Jan 27, 2025

Hi, I can't found solution to downgrade ccp4.
I run singularity exec --no-home --bind /data/result_all_vs_all:/mnt ~/Downloads/ccp4-9/fold_analysis_latest_withCCP4.sif run_get_good_pae.sh --output_dir=/mnt --cutoff=10

Log files don't show problems.

log_fold_analysis.txt

I don't know when run_pi_score.py/.sh are used.

@DimaMolod DimaMolod added the bug Something isn't working label Jan 27, 2025
@DimaMolod DimaMolod added this to the Priority1 milestone Jan 27, 2025
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