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integrativemodeling / mediator

Modeling of the yeast Mediator complex
https://salilab.org/mediator/
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Where are the output trajectories? #4

Closed benmwebb closed 7 years ago

benmwebb commented 7 years ago

Normally I would expect to see one or more directories with output models (prior to clustering), for example in an output subdirectory (here is the equivalent for the exosome modeling) but I don't see that for Mediator.

I'm sure that these trajectories are too big to fit in a GitHub repository, which is why they weren't uploaded in the first place. But I'd still like to have them for reference. We can upload them to Zenodo or (worst case) put them on the Sali lab's FTP site. Where are they?

benmwebb commented 7 years ago

@Pellarin @cgreenberg Any idea where these trajectories can be found?

benmwebb commented 7 years ago

Per Riccardo, most likely they are (somewhere) in /salilab/park1/pellarin/mediator.tar.xz

Pellarin commented 7 years ago

Yes, if we can untar that 30GB file somewhere, I can definitely look into it!

benmwebb commented 7 years ago

See /salilab/park1/pellarin/no-backup/mediator/.

Pellarin commented 7 years ago

in /salilab/park1/pellarin/no-backup/mediator/for_publication/analysis the directories clustering clustering_half1 clustering_half2 clustering_jackknifing contains the clustering analysis published in the paper. In each directory look the clustering.py file which contains the path of the original trajectories. For instance, for clustering/clustering.py you have:

"../../run20/modeling.split_density.scale_radii.two_bayesian_classes-1.1",
"../../run20/modeling.split_density.scale_radii.two_bayesian_classes-1.2",
"../../run20/modeling.split_density.scale_radii.two_bayesian_classes-1.3",
"../../run20/modeling.split_density.scale_radii.two_bayesian_classes-1.4",
"../../run28/modeling.split_density.scale_radii.two_bayesian_classes-1.5",
"../../run28/modeling.split_density.scale_radii.two_bayesian_classes-1.6",
"../../run28/modeling.split_density.scale_radii.two_bayesian_classes-1.7",
"../../run28/modeling.split_density.scale_radii.two_bayesian_classes-1.8",
"../../run31/modeling.split_density.scale_radii.two_bayesian_classes-1.9",
"../../run31/modeling.split_density.scale_radii.two_bayesian_classes-1.10",
"../../run31/modeling.split_density.scale_radii.two_bayesian_classes-1.11",
"../../run31/modeling.split_density.scale_radii.two_bayesian_classes-1.12",
"../../run31/modeling.split_density.scale_radii.two_bayesian_classes-1.13",
"../../run31/modeling.split_density.scale_radii.two_bayesian_classes-1.14",
"../../run31/modeling.split_density.scale_radii.two_bayesian_classes-1.15",
"../../run31/modeling.split_density.scale_radii.two_bayesian_classes-1.16",
"../../run31/modeling.split_density.scale_radii.two_bayesian_classes-1.17",
"../../run31/modeling.split_density.scale_radii.two_bayesian_classes-1.18",
"../../run31/modeling.split_density.scale_radii.two_bayesian_classes-1.19",
"../../run31/modeling.split_density.scale_radii.two_bayesian_classes-1.20"
benmwebb commented 7 years ago

Perfect, thanks Riccardo! I'll archive these directories at Zenodo - they're not too big.

Pellarin commented 7 years ago

Awesome! Thanks!