tskit.load returns "unknown file attribute: i" on macOS

[chlangley]

Hello:

Just trying to work through the Example in the documentation.
When I get to the tskit.load():

source = tskit.load("simulation-source.trees")
inferred = tskit.load("simulation.trees")

I get this
"zsh: unknown file attribute: i"

I trust I am ignorant of a simple python/tskit feature.
Thanks for any help.

Cheers,
Chuck

[petrelharp]

Well, that's a confusing error. This is in the tsinfer docs, so I'll transfer this over to tsinfer.

But, I've just tried out the code in the tutorial and not got the same problem. Maybe first make sure that tsinfer is up to date? And then check the file's in the directory your python is in, like:

os.path.isfile("simulation.trees")

Another check is to go to the terminal and check the .trees files are valid there:

tskit info simulation.trees

Let us know what happens?

[petrelharp]

That all seems in order - any ideas here @benjeffery @hyanwong?

[chlangley]

Does anyone think I should attempt a clean start, removing miniconda and all the ts modules?

And I should have mentioned that my macOS is v11.6 and hardware is MacBook Pro (16 inch, 2019).

The python3 is v 3.9.7 and conda -V 4.10.3.

Thanks for any help.
Cheers, Chuck

[hyanwong]

It should be easy to install a new miniconda distro somewhere else and try that? I'm stumped here: I've never seen that before and the internet is surprisingly unhelpful on this one.

[petrelharp]

Any other diagnostics you can think of? @chlangley what happens when you run tskit info simulation.trees and tskit info simulation-source.trees? (Also, which .trees file gives the error?)

[chlangley]

(base) ➜ playts ll
total 38888
-rw-r--r--@ 1 chuck admin 641B Sep 24 03:23 simulation-example.py
-rw-r--r-- 1 chuck admin 8.2M Sep 24 03:25 simulation-source.trees
-rw-r--r-- 1 chuck admin 22M Sep 24 03:25 simulation.samples
-rw-r--r-- 1 chuck admin 7.8M Sep 25 10:19 simulation.trees
(base) ➜ playts source = tskit.load("simulation-source.trees")
zsh: unknown file attribute: i
(base) ➜ playts inferred = tskit.load("simulation.trees")
zsh: unknown file attribute: i
(base) ➜ playts tskit info simulation.trees
sequence_length: 10000000.0
trees: 19838
samples: 10000
individuals: 10000
nodes: 37776
edges: 98601
sites: 38778
mutations: 38778
migrations: 0
populations: 0
provenances: 4
(base) ➜ playts

[petrelharp]

Ah-ha! I think the answer is simple - when I do that in zsh I get:

$ source = tskit.load("simulation-source.trees")
zsh: unknown file attribute

... which is almost the same error. However - the code chunk starting

import tskit

source = tskit.load("simulation-source.trees")
inferred = tskit.load("simulation.trees")

is supposed to be run in python, not the shell. Is this the problem? We haven't said explicitly that we're switching back to python here, I guess that we're expecting the user to pick up on the lack of $s at the start of the lines? Perhaps we should say "Going back to python," before that code chunk?

[chlangley]

yes. if I 'conda deactivate'. And then invoke python3, then I

import tskit

source = tskit.load("simulation-source.trees")
inferred = tskit.load("simulation.trees")

and all seems good.

So these tskit command can not be called with conda?

[benjeffery]

Note that conda activate does not start python, it only sets which python is avaliable. You need to run python3 to run any python code.

[hyanwong]

We can probably tidy the language in the tutorial to make it clearer. I'm happy to do this.

[hyanwong]

Can you mark this as the correct answer @chlangley ?

[hyanwong]

I've changed the tutorial wording @chlangley - could you see if it's clearer now that this needs to be run within python, rather than on the command line?

[chlangley]

Will do

…

On Sep 29, 2021, at 3:05 PM, Yan Wong ***@***.***> wrote:  I've changed the tutorial wording @chlangley - could you see if it's clearer now that this needs to be run within python, rather than on the command line? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.