david-castillo
commented
3 years ago Hi,
I checked it and the problem seems to come from one of the last updates (https://github.com/3DGenomes/TADdyn/blob/20f1ea8becf6de77cbe5a1e78c8dac545e9d0874/taddyn/modelling/lammps_modelling.py#L697) . Mainly the initial conformations should be returned at the beginning the dictionary of models (in the keys 0 to nkeep) but they are not, and that broke the test. I need to fix that.
David
Hello, After I installed the TADdyn, I wanna try the test data and run with this:
python2 test_TADdyn_on_Sox2.py
whereas the error logs shows like this:
Optimizing 300 particles num scale kbending maxdist lowfreq upfreq dcutoff correlation WARNING: not all models produced: step 1, nmodels=100 1 0.01 0 150 -3 0 100 0.477 2 0.01 0 150 -3 1 100 0.5725 3 0.01 0 150 -3 2 100 0.4501 4 0.01 0 150 -3 3 100 0.2003 5 0.01 0 150 -2 0 100 0.5026 6 0.01 0 150 -2 1 100 0.5823 7 0.01 0 150 -2 2 100 0.4504 8 0.01 0 150 -2 3 100 0.2003 9 0.01 0 150 -1 0 100 0.6097 10 0.01 0 150 -1 1 100 0.6358 11 0.01 0 150 -1 2 100 0.4508 12 0.01 0 150 -1 3 100 0.2 13 0.01 0 150 0 0 100 0.6122 14 0.01 0 150 0 1 100 0.6392 15 0.01 0 150 0 2 100 0.452 16 0.01 0 150 0 3 100 0.2026 17 0.01 0 200 -3 0 100 0.25 18 0.01 0 200 -3 1 100 0.552 19 0.01 0 200 -3 2 100 0.4392 20 0.01 0 200 -3 3 100 0.2033 21 0.01 0 200 -2 0 100 0.3219 22 0.01 0 200 -2 1 100 0.5702 23 0.01 0 200 -2 2 100 0.4384 ............................................................................................................ 94 0.01 0 400 0 1 100 0.4153 95 0.01 0 400 0 2 100 0.2748 WARNING: this is an empty shell, no data here. 96 0.01 0 400 0 3 100 0.1998 Succesfully generated tadbit initial conformation
Unknown error with process Unknown error with process Unknown error with process Unknown error with process Unknown error with process Unknown error with process Models analysis: 0 - Loading the models 1 - Z-score plots DONE 2 - Snapshots Traceback (most recent call last): File "/tools/Chr_simulation/TADdyn/test/Sox2/test_TADdyn_on_Sox2.py", line 91, in
sm.view_models(models=[int(stage100100)], tool="plot", savefig="./Results/Snapshots/Snapshot_trajectory_1timepoint%d.png" % int(stage*100))
File "/Miniconda3/envs/Chr_simulation/lib/python2.7/site-packages/pytadbit/modelling/structuralmodels.py", line 2165, in view_models
self[model]['x'], self[model]['y'], self[model]['z']))
File "/Miniconda3/envs/Chr_simulation/lib/python2.7/site-packages/pytadbit/modelling/structuralmodels.py", line 156, in getitem
return self.__models[nam]
KeyError: 10000
Did anyone know the reason and solution?