ASTRID ERROR

[Alexandre Pedro]

Dear Pranjal,

I may be missing something, but it doesn't seem to obvious to me. I am trying to run ASTRID but every time I download it is comes with the extension .dms. I have tried to extract this file with no success but I also tried to follow the chmod +x ASTRID-osx and the mv ASTRID-osx ASTRID commands on the .dms file. I keep getting this error message:

Failed to execute script ASTRID

Traceback (most recent call last):

  File "ASTRID.py", line 9, in <module>

  File "/Users/pranjal/Library/Python/2.7/lib/python/site-packages/PyInstaller/loader/pyimod03_importers.py", line 389, in load_module

  File "dendropy/__init__.py", line 24, in <module>

  File "/Users/pranjal/Library/Python/2.7/lib/python/site-packages/PyInstaller/loader/pyimod03_importers.py", line 389, in load_module

  File "dendropy/dataio/__init__.py", line 20, in <module>

  File "/Users/pranjal/Library/Python/2.7/lib/python/site-packages/PyInstaller/loader/pyimod03_importers.py", line 389, in load_module

  File "dendropy/dataio/newickreader.py", line 27, in <module>

  File "/Users/pranjal/Library/Python/2.7/lib/python/site-packages/PyInstaller/loader/pyimod03_importers.py", line 389, in load_module

  File "dendropy/utility/textprocessing.py", line 40, in <module>

  File "locale.py", line 543, in getdefaultlocale

  File "locale.py", line 475, in _parse_localename

ValueError: unknown locale: UTF-8

I am trying to run the most recent ASTRID version on a Mac OS Sierra (10.12).

Thanks in advance for your time and attention!

Alex

[p...@nj.al]

Thanks for letting me know - I have a new version of ASTRID that should fix these problems; I'll package it up and send it to you this weekend.

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[Sara Rocha]

Hi!

I just downloaded ASTRAL ( the osx binary from here: https://github.com/pranjalv123/ASTRID/releases) and got exactly this same error.

was this ever solved? with which binary ?

pasting my screenlog bellow. any help appreciatted, thanks! (trying to run in mojave 10.14.3)

saramac:ASTRID sara$ chmod +x ASTRID-osx 

saramac:ASTRID sara$ ./ASTRID-osx 

Failed to execute script ASTRID

Traceback (most recent call last):

  File "ASTRID.py", line 9, in <module>

  File "/Users/pranjal/Library/Python/2.7/lib/python/site-packages/PyInstaller/loader/pyimod03_importers.py", line 389, in load_module

  File "dendropy/__init__.py", line 24, in <module>

  File "/Users/pranjal/Library/Python/2.7/lib/python/site-packages/PyInstaller/loader/pyimod03_importers.py", line 389, in load_module

  File "dendropy/dataio/__init__.py", line 20, in <module>

  File "/Users/pranjal/Library/Python/2.7/lib/python/site-packages/PyInstaller/loader/pyimod03_importers.py", line 389, in load_module

  File "dendropy/dataio/newickreader.py", line 27, in <module>

  File "/Users/pranjal/Library/Python/2.7/lib/python/site-packages/PyInstaller/loader/pyimod03_importers.py", line 389, in load_module

  File "dendropy/utility/textprocessing.py", line 40, in <module>

  File "locale.py", line 543, in getdefaultlocale

  File "locale.py", line 475, in _parse_localename

ValueError: unknown locale: UTF-8

saramac:ASTRID sara$ 

[Sara Rocha]

ok, great, thanks! will try and let u know.

just one more thing:

am I interpreting well that to use the corrected version (better deal with missing data) mentioned in here:

https://github.com/adamallo/ASTRIDm

is now implemented in the main method and what I have to do is use -bionj? plus the --bygene for the "unweighted" version (AGID distances averaged by gene)

thanks in advance,

sara

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Sara Rocha

Post-Doc Researcher

Phylogenomics Group University of Vigo (Spain)
http://darwin.uvigo.es/sara-rocha/

On 5 Apr 2019, 02:00 +0200, Pranjal Vachaspati <m...@pranj.al>, wrote:

Hi Sara,

Please try the release for ASTRID-2 at 

https://github.com/pranjalv123/ASTRID-2/releases/tag/0.1

This has been optimized for better performance and easier installation. You may need to install Java on your system for it to work (but OS X will suggest this if it is the case). 

Let me know if it works or not.

Thanks,

Pranjal

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[Pranjal Vachaspati]

I am actually unfamiliar with this forked version of ASTRID. This looks to be based on the older, Python version of ASTRID (ASTRID-1), so if you had problems running that, you may have problems running this as well. 

You would have to check with the author of that release (he may be on this list), but I believe that the primary difference between that version of ASTRID and this one is that it supports multiple individuals per species.

If you have only one individual per species, you can use ASTRID-2, and you should not probably not use any options, just do

ASTRID -i <inputtrees> -o <outputfile>

It will automatically pick the best distance method.

[Sara Rocha]

right… ok, thing is that I do have missing data (and multiple, not completely overlapping individuals per species). I will check with the author of the forked version, thanks a lot!

--

Sara Rocha

Post-Doc Researcher

Phylogenomics Group University of Vigo (Spain)
http://darwin.uvigo.es/sara-rocha/

[Pranjal Vachaspati]

Currently, ASTRID-2 works with missing data, but not with multiple individuals per species. You could run it treating each individual as a species, and you would get back a species tree with each individual in it. You could also pick a representative individual for each species.

[Sara Rocha]

Hi again,

similar error with linux binary. any help really appreciated. thanks in advance!

[srocha@triploid astrid_pod]$ ./ASTRID-linux 

Traceback (most recent call last):

  File "ASTRID", line 9, in <module>

  File "/home/vachasp2/.local/lib/python2.7/site-packages/PyInstaller-3.3.dev0+gd25657e.mod-py2.7.egg/PyInstaller/loader/pyimod03_importers.py", line 389, in load_module

  File "dendropy/__init__.py", line 24, in <module>

  File "/home/vachasp2/.local/lib/python2.7/site-packages/PyInstaller-3.3.dev0+gd25657e.mod-py2.7.egg/PyInstaller/loader/pyimod03_importers.py", line 389, in load_module

  File "dendropy/dataio/__init__.py", line 20, in <module>

  File "/home/vachasp2/.local/lib/python2.7/site-packages/PyInstaller-3.3.dev0+gd25657e.mod-py2.7.egg/PyInstaller/loader/pyimod03_importers.py", line 389, in load_module

  File "dendropy/dataio/newickreader.py", line 27, in <module>

  File "/home/vachasp2/.local/lib/python2.7/site-packages/PyInstaller-3.3.dev0+gd25657e.mod-py2.7.egg/PyInstaller/loader/pyimod03_importers.py", line 389, in load_module

  File "dendropy/utility/textprocessing.py", line 40, in <module>

  File "locale.py", line 543, in getdefaultlocale

  File "locale.py", line 475, in _parse_localename

ValueError: unknown locale: UTF-8

Failed to execute script ASTRID

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Sara Rocha

Post-Doc Researcher

Phylogenomics Group University of Vigo (Spain)
http://darwin.uvigo.es/sara-rocha/

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