only run summary report?

[grandrea]

Hi, I have a bunch of jobs that keep crashing. I would like to resubmit the whole snakemake run, but only running summary report generation, so that those jobs are skipped rather than submitted. Is it possible? Do you advise doing this another way?

[DimaMolod]

Hi @grandrea, with a recent AlphaPulldownSnakemake version, AlphaJudge is already available through the analysis container. Running the report through Snakemake would resubmit failed jobs because the report depends on every fold.

To summarise only the usable completed runs, invoke AlphaJudge directly: either install it with pip install alphajudge or use the container:

mkdir -p <output_directory>/reports
apptainer exec docker://kosinskilab/alphajudge:latest \
  alphajudge <output_directory>/predictions --recursive \
  --summary <output_directory>/reports/all_interfaces_completed.csv

Use singularity exec instead if appropriate. Incomplete runs that AlphaJudge cannot process will not be included.