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CovertLab / wcEcoli

Whole Cell Model of E. coli
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Anaerobic Daily Build Failures #659

Closed tahorst closed 4 years ago

tahorst commented 5 years ago

Can someone look into it?

prismofeverything commented 5 years ago 
Traceback (most recent call last):
  File "/home/groups/mcovert/pyenv/versions/wcEcoli2/lib/python2.7/site-packages/fireworks/core/rocket.py", line 262, in run
    m_action = t.run_task(my_spec)
  File "/scratch/groups/mcovert/jenkins/workspace@2/wholecell/fireworks/firetasks/simulationDaughter.py", line 53, in run_task
    sim.run()
  File "/scratch/groups/mcovert/jenkins/workspace@2/wholecell/sim/simulation.py", line 224, in run
    self.run_incremental(self._lengthSec + self.initialTime())
  File "/scratch/groups/mcovert/jenkins/workspace@2/wholecell/sim/simulation.py", line 247, in run_incremental
    self._evolveState()
  File "/scratch/groups/mcovert/jenkins/workspace@2/wholecell/sim/simulation.py", line 291, in _evolveState
    process.calculateRequest()
  File "/scratch/groups/mcovert/jenkins/workspace@2/models/ecoli/processes/transcript_initiation.py", line 115, in calculateRequest
    TU_index, bound_TF = self.promoters.attrs("TU_index", "bound_TF")
  File "/scratch/groups/mcovert/jenkins/workspace@2/wholecell/states/unique_molecules.py", line 248, in attrs
    return self._queryResult.attrs(*attributes)
  File "/scratch/groups/mcovert/jenkins/workspace@2/wholecell/containers/unique_objects_container.py", line 912, in attrs
    self.attr(attribute) for attribute in attributes
  File "/scratch/groups/mcovert/jenkins/workspace@2/wholecell/containers/unique_objects_container.py", line 912, in <genexpr>
    self.attr(attribute) for attribute in attributes
  File "/scratch/groups/mcovert/jenkins/workspace@2/wholecell/containers/unique_objects_container.py", line 877, in attr
    raise UniqueObjectsContainerException("Object set is empty")
UniqueObjectsContainerException: Object set is empty
ggsun commented 5 years ago

This looks like something I should be responsible for. I’ll look into it when I get to the lab in the afternoon.

ggsun commented 5 years ago

After #663, this now fails because some of the analyses scripts fail with cells with no chromosomes:

Traceback (most recent call last):
  File "/scratch/groups/mcovert/jenkins/workspace@2/wholecell/fireworks/firetasks/analysisBase.py", line 163, in run_task
    mod.Plot.main(*args)
  File "/scratch/groups/mcovert/jenkins/workspace@2/models/ecoli/analysis/analysisPlot.py", line 126, in main
    validationDataFile, metadata)
  File "/scratch/groups/mcovert/jenkins/workspace@2/models/ecoli/analysis/analysisPlot.py", line 116, in plot
    validationDataFile, metadata)
  File "/scratch/groups/mcovert/jenkins/workspace@2/models/ecoli/analysis/single/mRnaHalfLives.py", line 123, in do_plot
    maxLine = 1.1 * max(max(expectedDegR), max(predictedDegR))
ValueError: max() arg is an empty sequence
Traceback (most recent call last):
  File "/scratch/groups/mcovert/jenkins/workspace@2/wholecell/fireworks/firetasks/analysisBase.py", line 163, in run_task
    mod.Plot.main(*args)
  File "/scratch/groups/mcovert/jenkins/workspace@2/models/ecoli/analysis/analysisPlot.py", line 126, in main
    validationDataFile, metadata)
  File "/scratch/groups/mcovert/jenkins/workspace@2/models/ecoli/analysis/analysisPlot.py", line 116, in plot
    validationDataFile, metadata)
  File "/scratch/groups/mcovert/jenkins/workspace@2/models/ecoli/analysis/single/replication.py", line 97, in do_plot
    ax.set_ylim([np.around(criticalMassEquivalents[1:].min(), decimals=1) - 0.1, np.around(criticalMassEquivalents[1:].max(), decimals=1) + 0.1])
  File "/home/groups/mcovert/pyenv/versions/wcEcoli2/lib/python2.7/site-packages/matplotlib/axes/_base.py", line 3429, in set_ylim
    bottom = self._validate_converted_limits(bottom, self.convert_yunits)
  File "/home/groups/mcovert/pyenv/versions/wcEcoli2/lib/python2.7/site-packages/matplotlib/axes/_base.py", line 3040, in _validate_converted_limits
    raise ValueError("Axis limits cannot be NaN or Inf")
ValueError: Axis limits cannot be NaN or Inf
ggsun commented 5 years ago

The daily builds have somehow been saved after the recent pushes, but the underlying problem of some cells not being able to double its mass within our time limit still needs to be resolved.

tahorst commented 4 years ago

I think #666 catches if we don't double in time and this is no longer an issue.