salilab / imp_analysis_tutorial Goto Github PK

It's very interesting.
Here's what I did so far.

1. Simply executed run_analysis_trajectories.py with ../modeling/ example (as results are provided in this repo).
   this gives no value error or anything but smoothly finish up.
2. performed the sampling with the same data and modeling.py with same 8 5000. Iteration was finished just fine.
   When I performed run_analysis_trajectories.py with ../modeling/ smaller (which is the modeling i just executed)
   I'm getting the following output with error msg. Does it indicate that there's an issue with modeling?
   I tested with conda version and manually compiled version. Both save me more or less consistent result with same type of value error msg.

$ python ./run_analysis_trajectories.py ../modeling/ smaller
The mean score, min score, and n frames are: 1 588.325948240789 561.0772547632217 5000
Trajectory, ts_eqs: smaller1 [200, 0, 3400, 0]
The mean score, min score, and n frames are: 6 602.5281745176727 578.3488141088378 5000
Trajectory, ts_eqs: smaller6 [0, 200, 0, 0]
The mean score, min score, and n frames are: 2 632.6239315579007 608.8117325905234 5000
Trajectory, ts_eqs: smaller2 [0, 200, 1600, 0]
The mean score, min score, and n frames are: 8 591.0158963523896 565.5735195176985 5000
Trajectory, ts_eqs: smaller8 [600, 600, 2000, 0]
The mean score, min score, and n frames are: 5 inf inf 5000
/cm/shared/apps/python-3.7.7/lib/python3.7/site-packages/numpy/core/_methods.py:193: RuntimeWarning: invalid value encountered in subtract
x = asanyarray(arr - arrmean)
/home/kim/conda_imp/original/imp_analysis_tutorial/rnapolii/analysis/../../lib/PMI_analysis/pyext/src/equilibration.py:101: RuntimeWarning: invalid value encountered in subtract
dA_n = A_n.astype(np.float64) - mu_A
/home/kim/conda_imp/original/imp_analysis_tutorial/rnapolii/analysis/../../lib/PMI_analysis/pyext/src/equilibration.py:102: RuntimeWarning: invalid value encountered in subtract
dB_n = B_n.astype(np.float64) - mu_B
Trajectory, ts_eqs: smaller5 [0, 0, 3800, 0]
Process Process-2:
Traceback (most recent call last):
File "/cm/shared/apps/python-3.7.7/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/cm/shared/apps/python-3.7.7/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/home/kim/conda_imp/original/imp_analysis_tutorial/rnapolii/analysis/../../lib/PMI_analysis/pyext/src/analysis_trajectories.py", line 553, in read_traj_info
self.plot_scores_restraints(S_tot_scores[['MC_frame']+sel_entries], ts_eq, file_out)
File "/home/kim/conda_imp/original/imp_analysis_tutorial/rnapolii/analysis/../../lib/PMI_analysis/pyext/src/analysis_trajectories.py", line 627, in plot_scores_restraints
n_bins, histtype='step',fill=False, color='orangered',alpha=0.9)
File "/cm/shared/apps/python-3.7.7/lib/python3.7/site-packages/matplotlib/init.py", line 1565, in inner
return func(ax, *map(sanitize_sequence, args), **kwargs)
File "/cm/shared/apps/python-3.7.7/lib/python3.7/site-packages/matplotlib/axes/_axes.py", line 6649, in hist
m, bins = np.histogram(x[i], bins, weights=w[i], **hist_kwargs)
File "<array_function internals>", line 6, in histogram
File "/cm/shared/apps/python-3.7.7/lib/python3.7/site-packages/numpy/lib/histograms.py", line 795, in histogram
bin_edges, uniform_bins = _get_bin_edges(a, bins, range, weights)
File "/cm/shared/apps/python-3.7.7/lib/python3.7/site-packages/numpy/lib/histograms.py", line 429, in _get_bin_edges
first_edge, last_edge = _get_outer_edges(a, range)
File "/cm/shared/apps/python-3.7.7/lib/python3.7/site-packages/numpy/lib/histograms.py", line 319, in _get_outer_edges
"supplied range of [{}, {}] is not finite".format(first_edge, last_edge))
ValueError: supplied range of [inf, inf] is not finite
All available fields: ['MC_frame' 'rmf_frame_index' 'Total_Score' 'XLs_Trnka' 'XLs_Chen'
'XLs_psi_Trnka' 'XLs_psi_Chen' 'CR_Rpb2' 'CR_Rpb11' 'CR_Rpb3' 'CR_Rpb9'
'CR_Rpb10' 'CR_Rpb6' 'CR_Rpb12' 'CR_Rpb8' 'CR_Rpb1' 'CR_Rpb4' 'CR_Rpb7'
'CR_Rpb5' 'EV_sum' 'GaussianEMRestraint_None'
'GaussianEMRestraint_None_CCC' 'GaussianEMRestraint_sigma_None' 'traj'
'rmf3_file' 'XLs_sum' 'CR_sum' 'half']
Number of unique clusters: 3 [-1 0 1]
Generating HDBSCAN clustering plot ...
Selecting and writing models to extract ...
Clustering summary:
Total_Score EV_sum XLs_sum GaussianEMRestraint_None N_models N_A N_B
cluster
1 593.346315 300.079624 144.830518 145.810335 5823 527 5296
0 626.219631 328.401122 145.844188 148.907098 2032 6 2026
-1 636.248459 326.632034 149.667570 152.847302 945 67 878
Summarize XLs, unique_clusters [-1 0 1]

If you have any insights what might've caused the issue and prevent this, I would really appreciate your help.

Thank you so much.

best,
hee jong

Hi,

I would like to perform the computational expensive modeling.py across multiple nodes.
However, it seems like modeling.py with its associated script is made for a single machine.
Do you have any examples or recommendations how to accomplish that?
I assume that i need to use mpi but I'm not sure how to properly modify to maximize the speed, efficiency, and replica exchange across nodes.

Thanks.

best,
hee jong

The uploaded localization density files here are empty. Running sampcon's exhaust according to this tutorial also results in empty mrc files. Perhaps the density.txt is not correct, because exhaust otherwise runs fine.

Hi,

I got some test-drive runs from my own benchmark dataset via modeling.py

However, when i attempt to execute run_analysis_trajectories.py, i repeatedly getting the following error and eventually it failed with get_psi_stats part with "IndexError: list index out of range" because the list is empty.

It seems fine to provide the right traj and stat_files to read_stats_detailed function but
S_score and S_dist are empty list so it causes error with "Get distance fields" and so on.

Process Process-2:
Traceback (most recent call last):
File "/cm/shared/apps/python-3.7.7/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/cm/shared/apps/python-3.7.7/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/home/kim/imp_single_node_test/imp_analysis_tutorial/rnapolii_01_50_100/analysis/../../lib/PMI_analysis/pyext/src/analysis_trajectories.py", line 527, in read_traj_info
stat_files)
File "/home/kim/imp_single_node_test/imp_analysis_tutorial/rnapolii_01_50_100/analysis/../../lib/PMI_analysis/pyext/src/analysis_trajectories.py", line 468, in read_stats_detailed
S_dist = S_dist[S_dist[:,0].argsort()]
IndexError: too many indices for array

Is there a way to take a look at this in a different angle to troubleshoot where it got messed up?
I suspect that it could be the output file itself but I don't have a good understanding to tell whether it's ok or not.

Thanks.