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dereneaton
Object 'quartets' does not exist
I've encountered an error when trying to restart a tetrad run that failed because the Jupyter notebook shut down/restarted. The full error is posted below, and occurs immediately after restarted (after running tet.run(auto = True)). The analysis-tetrad folder is unchanged from when the run stopped, and the *quartets.txt file is still present with the correct number of lines: nquartets and wc -l *.quartets.txt both equal 20e6.
Is this a permissions issue? An issue with directing ipyrad where to look for the quartets file upon reset? Any help you have would be great. Thanks!
Running ipyrad version 0.9.81 on Jupyter (4.5.0) notebook (5.2.2) on a Linux (Ubuntu 20.04) desktop.
Parallel connection | alex-desktop: 4 cores
[ ] 0% 0:00:01 | boot rep. 2
Encountered an Error.
Message: KeyError: "Unable to open object (object 'quartets' doesn't exist)"
Use debug flag (-d) for full code traceback.
---------------------------------------------------------------------------KeyError Traceback (most recent call last)<string> in <module>()
/home/alex/miniconda3/envs/ipyrad/lib/python3.6/site-packages/tetrad/worker.py in nworker(tet, chunk)
69 seqview = io5["bootsarr"][:]
70 maparr = io5["bootsmap"][:, 0]
---> 71 smps = io5["quartets"][chunk:chunk + tet._chunksize]
72
73 # create an N-mask array of all seq cols
h5py/_objects.pyx in h5py._objects.with_phil.wrapper()
h5py/_objects.pyx in h5py._objects.with_phil.wrapper()
/home/alex/miniconda3/envs/ipyrad/lib/python3.6/site-packages/h5py/_hl/group.py in __getitem__(self, name)
262 raise ValueError("Invalid HDF5 object reference")
263 else:
--> 264 oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
265
266 otype = h5i.get_type(oid)
h5py/_objects.pyx in h5py._objects.with_phil.wrapper()
h5py/_objects.pyx in h5py._objects.with_phil.wrapper()
h5py/h5o.pyx in h5py.h5o.open()
KeyError: "Unable to open object (object 'quartets' doesn't exist)"
You need to use tet.run(auto = True, force=True).
If the jupyter notebook shutdown hard then it's possible the "quartets" dataset wasn't saved to the h5py file. You'll have to force recreating it unfortunately. Tetrad is more Deren's creation, so he might have more to say here.
If I use force = True, all my progress will be lost right? At 16 hours to
run the initial tree, and 5 hours per bootstrap, I'd really prefer to
continue where I left off if possible. I also don't really know why jupyter
notebook shut down, so I have no guarantees that this won't happen again
after the second bootstrap. Is there any way to rewrite just the quartet
file?
On Mon, Sep 20, 2021 at 9:42 AM Isaac Overcast @.***> wrote:
You need to use tet.run(auto = True, force=True).
If the jupyter notebook shutdown hard then it's possible the "quartets" dataset wasn't saved to the h5py file. You'll have to force recreating it unfortunately. Tetrad is more Deren's creation, so he might have more to say here.
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I see your point. This is really a better question for Deren. I can probably figure it out, but I won't be able to look at it until I get past a couple very imminent deadlines, maybe later this week.
Notebooks crashing are often memory allocation issues. If the system runs out of RAM because the notebook process chews it all up then this can cause a crash.