Scott T Small comments

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                                            Scott T Small

Error in rule plot_synteny_nocolor

I fixed this by adding `matplotlib.use('agg')` to the file in PATH/scripts/odp at line 48

lmdb out of memory error on tutorial example

Hi, Sorry for the quick edit. I am working on Linux machine. thanks, @stsmall

lmdb out of memory error on tutorial example

specifically: AME="Red Hat Enterprise Linux Server" VERSION="7.9 (Maipo)"

lmdb out of memory error on tutorial example

In [3]: ts.num_sites Out[3]: 39001 In [4]: ts.num_samples Out[4]: 10000 yes, loading the tree sequence seems to work In [5]: tsinfer.SampleData.from_tree_sequence(ts) Out[5]: oddly if I run this: tsinfer.SampleData.from_tree_sequence(ts, path="simulation_samples", num_flush_threads=2)...

lmdb out of memory error on tutorial example

disk space ... 5T

lmdb out of memory error on tutorial example

OK, I will try that and let you know.

lmdb out of memory error on tutorial example

Successfully installed lmdb-1.0.0 Successfully installed zarr-2.5.0 Didnt seem to make a difference and I still am getting the memory error.

lmdb out of memory error on tutorial example

seems to be specific to using the path keyword tsinfer.SampleData.from_tree_sequence(ts, num_flush_threads=2) # no error tsinfer.SampleData.from_tree_sequence(ts, path="samples", num_flush_threads=2) # memory error

lmdb out of memory error on tutorial example

If I run from the command line version on the trees from msprime: $ tsinfer infer simulation-source.trees 2020-10-20 15:35:37,373 [32391] CRITICAL root: Traceback (most recent call last): File "anaconda3/envs/allel/lib/python3.7/site-packages/tsinfer/formats.py", line...

lmdb out of memory error on tutorial example

Sorry about that, I was trying everything :) I edited to remove the identifying info. The scratch space is where I have 5T of empty space. I have had some...