josephwb
commented
6 years ago Sorry but that is unreadable! Do you have the newicks for both input and output?
Closed Cactusolo closed 6 years ago
josephwb
commented
6 years ago Sorry but that is unreadable! Do you have the newicks for both input and output?
Cactusolo
commented
6 years ago Yes, here is the input file: 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On May 14, 2018, at 14:26, Joseph W. Brown notifications@github.com wrote:
Sorry but that is unreadable! Do you have the newicks for both input and output?
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josephwb
commented
6 years ago As far as I can see all knuckles are removed.
$ pxlstr -t phy.tre
tree #: 0
rooted: false
binary: false
nterminal: 589
ninternal: 1943
branch lengths: false
rttipvar: NA
treelength: NA
ultrametric: NA
rootheight: NA
$pxlstr -t clean.tre
tree #: 0
rooted: true
binary: false
nterminal: 589
ninternal: 435
branch lengths: false
rttipvar: NA
treelength: NA
ultrametric: NA
rootheight: NAAs for the node names: phyx treats names and annotations differently. I may not have implemented this fully. Should be a quick fix.
Cactusolo
commented
6 years ago Ok, thanks Joseph!
Looking forward to new update then :)
Miao
On May 14, 2018, at 16:12, Joseph W. Brown notifications@github.com wrote:
As far as I can see all knuckles are removed.
$ pxlstr -t phy.tre tree #: 0 rooted: false binary: false nterminal: 589 ninternal: 1943 branch lengths: false rttipvar: NA treelength: NA ultrametric: NA rootheight: NA
$pxlstr -t clean.tre tree #: 0 rooted: true binary: false nterminal: 589 ninternal: 435 branch lengths: false rttipvar: NA treelength: NA ultrametric: NA rootheight: NA As for the node names: phyx treats names and annotations differently. I may not have implemented this fully. Should be a quick fix.
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josephwb
commented
6 years ago Yup this was a loose end https://github.com/FePhyFoFum/phyx/issues/73#issuecomment-381170370. Will fix it this evening. Sorry about the trouble.
josephwb
commented
6 years ago Actually I will get to this tomorrow.
Cactusolo
commented
6 years ago Take your time buddy!
No rush ;)
Miao
On May 14, 2018, at 16:50, Joseph W. Brown notifications@github.com wrote:
Actually I will get to this tomorrow.
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josephwb
commented
6 years ago Oof. Should be working with this 940b92702fd0d04036dbb27ff0ef8619df3d76c6.
josephwb
commented
6 years ago @Cactusolo please close if this works for you.
Cactusolo
commented
6 years ago Hi,
SoI need to update phyx package on my side from github, and then run again, right?
Thanks!
Miao
2018-05-15 12:15 GMT-04:00 Joseph W. Brown notifications@github.com:
@Cactusolo https://github.com/Cactusolo please close if this works for you.
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-- Dr. Miao Sun Tel: 352 (284) 0928 Email: cactus@ufl.edu Solti Lab, Florida Museum of Natural History, University of Florida Dickinson Hall, 1659 Museum Rd, PO. Box 117800, Gainesville, FL 32611-7800, USA.
Cactusolo
commented
6 years ago Hi,
I just realized that I have to request for update phyx on our HPC.
I'll report to you soon,
Miao
2018-05-15 13:14 GMT-04:00 Miao Sun notifications@github.com:
Hi,
SoI need to update phyx package on my side from github, and then run again, right?
Thanks!
Miao
2018-05-15 12:15 GMT-04:00 Joseph W. Brown notifications@github.com:
@Cactusolo https://github.com/Cactusolo please close if this works for you.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/FePhyFoFum/phyx/issues/82#issuecomment-389225815, or mute the thread https://github.com/notifications/unsubscribe-auth/AHczAIMGE8U440K- CoyEyHVsC5nfnNggks5tyv86gaJpZM4T-Rwu .
-- Dr. Miao Sun Tel: 352 (284) 0928 Email: cactus@ufl.edu Solti Lab, Florida Museum of Natural History, University of Florida Dickinson Hall, 1659 Museum Rd https://maps.google.com/?q=1659+Museum+Rd&entry=gmail&source=g, PO. Box 117800, Gainesville, FL 32611-7800, USA.
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-- Dr. Miao Sun Tel: 352 (284) 0928 Email: cactus@ufl.edu Solti Lab, Florida Museum of Natural History, University of Florida Dickinson Hall, 1659 Museum Rd, PO. Box 117800, Gainesville, FL 32611-7800, USA.
josephwb
commented
6 years ago Got it. Although most phyx programs are so lightweight and only run on a single core that I don't see any advantage in putting it on a cluster. But cool that you are!
Cactusolo
commented
6 years ago Thanks man! It works perfectly! 💯 👍
PS, I did most of my work remotely. Though I have home-brewed phyx on my mac, which conveniently not with me today :)
Cactusolo
commented
6 years ago @josephwb I close this issue now, thanks for all the help!
Hi,
I was told that "pxcltr" is meant to remove 'knuckles' (i.e. 2-degree nodes), node annotations, etc, to keep a plain format.
However, I used cmd like:
pxcltr -l -t Coweeta_ottid_nw_rename.treandpxcltr -t Coweeta_ottid_nw_rename.treBut the results are the same, still keeping some internal labels, eg:
...
Please let me know if you need tree file.
Thanks!