Unknown error with process

[poflawless]

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_1_timepoint_%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?

[david-castillo]

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