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chrisquince / STRONG

Strain Resolution ON Graphs
MIT License
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bayesgraph fail on SyntheticCommunity32/Seb_Debug2 merged bin #57

Open Sebastien-Raguideau opened 5 years ago

Sebastien-Raguideau commented 5 years ago

The Test dataset is handy but I can't debug merging event with it. So I've been using SyntheticCommunity32 also. Not sure if this is the new pipeline or an issue with bayesgraph. I'm going to start rerunning current pipeline with results from june and check for discrepancy.
If you have time, Chris, can you have a quick look? Here are the logs : /mnt/gpfs/Hackathon/SyntheticCommunity32/Seb_Debug2/bayespaths/Logs/Bin_merged_1_simplif.log

chrisquince commented 5 years ago

What version of BayesAGraphSVA are you using, can you make sure it is up to date with?

git submodule foreach git pull origin master

Sebastien-Raguideau commented 5 years ago

It seems to run, so it was just an outdated version of BayesAGraphSVA. This is cool. I'll relaunch from scratch and if everything works I propose we merge tomorrow.

Sebastien-Raguideau commented 5 years ago

It failed again. Though only after running for quite some time. It is the same bin and the log are still at : /mnt/gpfs/Hackathon/SyntheticCommunity32/Seb_Debug2/bayespaths/Logs/Bin_merged_1_simplif.log

File "/mnt/gpfs/Hackathon/STRONG/BayesAGraphSVA/AssemblyPath/AssemblyPathSVAS.py", line 1617, in sampleMargPath selectIn = self.prng.choice(np.arange(NC), 1, p=tempProb) File "mtrand.pyx", line 1144, in mtrand.RandomState.choice ValueError: probabilities contain NaN

At that point I think this is a BayesAGraphSVA issue more than a pipeline issue.

chrisquince commented 5 years ago

I agree this looks like a BayesAGraphSVA issue and I will debug it.

One thought though is do we want to reengineer the pipeline so that it does not break if one BayesAGraphSVA run fails but continues with the rest of the pipeline? We can discuss that this afternoon.

Sebastien-Raguideau commented 5 years ago

Are we skyping? That is easy to do, it's a snakemake option, we can add it permanently .