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    bredelings on faster-solver

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  • Sep 08 14:12
    bredelings commented #52
  • Sep 08 00:48
    snacktavish commented #52
Mark T. Holder
@mtholder
I think the files in https://files.opentreeoflife.org/synthesis/opentree12.3/output/cleaned_ott/ have the complement - the OTT IDs pruned
you can get them from an otcetera tool:
otc-count-leaves -l PARENT_OF_SYNTH_OUT/opentree12.3/labelled_supertree/labelled_supertree.tre
which takes about 4 seconds on my machine.
It's possible that the leaf list is somewhere else in the synth archive, but I can't remember it being anywhere.
Benjamin Redelings
@bredelings
That sounds like the best way to get the leaves.
You can also use time otc-tree-tool --show-leaves ~/Devel/OpenTree/synth-trees/opentree12.3/labelled_supertree/labelled_supertree.tre > leaves. The only difference is that the leaves look like "ott47378" versus "47378".
Emily Jane McTavish
@snacktavish
Ah nice! I ended up reading it into dendropy, which took a few min, but wasn't terrible. That seems much quicker for future though. (although I'd have to compile otcetera on my machine, so maybe not :P)
Benjamin Redelings
@bredelings
@snacktavish Compiling otcetera without the http stuff (restbed lib) should be pretty easy.
Benjamin Redelings
@bredelings
sudo apt install libboost-all-dev 
sudo apt install meson ninja-build # or `pip install meson ninja`
git clone git@github.com:OpenTreeOfLife/otcetera.git
cd otcetera
meson build -Dwebservices=false -Dprefix=<directory>
cd build
ninja install
Benjamin Redelings
@bredelings
I suppose we should add that to the README.md
Emily Jane McTavish
@snacktavish
ooh ya! That does sound handy.
Ive been playing with vis!
Here is a tree of all families in OpenTree (around 9,000), with overlays that show the number of studies supporting and conflicting with each branch.
the color max is for 5 studies (in support or conflict), although the numbers actually go up to 15-17
Emily Jane McTavish
@snacktavish
Karen Cranston
@kcranston
Cool - thanks for the link. I don't see any mention of changes in format, so this shouldn't (hopefully) affect our ability to update OTT.
Emily Jane McTavish
@snacktavish
very cool!
Jonathan A Rees
@jar398
Y'all follow Nico Franz on Twitter, yes? If not: https://twitter.com/taxonbytes/status/1302053367229816832 Job alert @asuSOLS; please retweet. Our Biodiversity Data Science initiative (incl. @beckettws @n8_upham) is recruiting a postdoc with strong computer science skills to develop taxonomically intelligent solutions for biodiversity. https://apply.interfolio.com/78177
Emily Jane McTavish
@snacktavish
Rapid climate change results in long-lasting spatial homogenization of phylogenetic diversity
Interesting work!
Mark T. Holder
@mtholder
hmm. otcetera-based ws are not running on API (which is causing the test failure)
I'll try rebooting
Mark T. Holder
@mtholder
hmm. didn't quite work. had to copy the conf from BAK
might be caching so redeployed phylesystem-api
that also needed some tweaks
Mark T. Holder
@mtholder
it seems to be back.
had to correct the user name from opentree to phylesystemapi
for the caching machine to work
Emily Jane McTavish
@snacktavish
Nice catch, I just now saw it was down.
@LunaSare was running a ton of conflict calls, I wondered if one might have caused an issue?
Mark T. Holder
@mtholder
perhaps. I did not see a particular problem in the logs, but I didn't look hard
Benjamin Redelings
@bredelings
it looks like otcetera web services crashed. I think we can find the last request before the crash and figure out the cause. I will look tomorrow.
Luna Luisa Sanchez Reyes
@LunaSare
Oh no 😰 I hope I didn’t break anything 😅
Benjamin Redelings
@bredelings
@LunaSare Looks like it was an otcetera crash on input that it didn't like. It wasn't a crash from too much use, I don't think.
It looks like the offending input was the newick tree '((((node5:5.1,node6:5.1)node4:1.2,node7:6.3)node3:7.5,node8:13.8)node2:11.5,node9:25.3)node1;'
This notably has no OTT labels on the tips.
It looks that this is the result of running conflict against ot_1876
WHich contains 5 primates, none of them mapped. Will investigate.
Luna Luisa Sanchez Reyes
@LunaSare
oh, yeah, that’s when my last conflict call stopped
I was running conflict for each chronogram in phylesystem
Thanks for the update Ben!
Emily Jane McTavish
@snacktavish
Ah, Luna and I were wondering what would happen if we ran it on a tree with no mapped taxa! Guess we found out :P
Mark T. Holder
@mtholder
call now-ish
Eschenholz
@eschenholz_twitter
hi, i found a misplaced group on the tree. is here the right place to talk about that?
Emily Jane McTavish
@snacktavish
Hi @eschenholz_twitter! You can comment on the node, to flag that information, or even better, upload a published tree to the study curator https://tree.opentreeoflife.org/curator that places the taxon in the right place!
Eschenholz
@eschenholz_twitter
thank you, i'll comment