Taxa substitution failed due to unknown error

[Fabian Kellner]

When trying to substitute taxa this error is displayed:

Failed to substitute taxa due to an unknown error. Possibly a bug. Please report on Launchpad.
Traceback (most recent call last):
  File "C:\Python27\lib\site-packages\supertree_toolkit-2.0-py2.7.egg\stk_gui\interface.py", line 2297, in on_sub_taxa_sub_taxa_button
  File "C:\Python27\lib\site-packages\supertree_toolkit-2.0-py2.7.egg\stk\supertree_toolkit.py", line 1678, in substitute_taxa
  File "C:\Python27\lib\site-packages\supertree_toolkit-2.0-py2.7.egg\stk\supertree_toolkit.py", line 3265, in _swap_tree_in_XML
ValueError: invalid literal for int() with base 10: 'NO'

[Jon Hill (jon-hill)]

Thanks for the report. I'll take a look. Can you attach the Phyml and the substitutions file (or the substitution you were trying to do) here so I can try and replicate this?

Thanks,

Jon

[Fabian Kellner (fabianlk)]

Thanks for the quick reply! Files are attached.
- Fabian

[Jon Hill (jon-hill)]

Super. Thanks. I'll try and get this looked at this week.
J.

[Jon Hill (jon-hill)]

Bug is caused by assuming tree names are in the form sourceName_n where n is an integer. This is a long-standing bug. Fix is to replace this code with more generic searches in _swap_tree_in_xml

[Jon Hill (jon-hill)]

Fix committed in: https://github.com/supertree-toolkit/stk/tree/fix_lp1703354

Tried the substitution on the submitter's data and it worked ok producing fewer taxa, but some are now permutable trees (contain %1, etc).

[Fabian Kellner (fabianlk)]

Thanks for the quick help John! The github link is not working (for me) though...

- Fabian

[Jon Hill (jon-hill)]

Sorry - I merged it into master and deleted the branch: https://github.com/supertree-toolkit/stk

I'll try and create a new .deb file (and Windows/Mac releases) soon.

[Fabian Kellner (fabianlk)]

Thank you very much :)

[Ruyue (moon1996)]

Failed to substitute taxa due to an unknown error. Possibly a bug. Please report on Launchpad.
Traceback (most recent call last):
  File "C:\Python27\lib\site-packages\supertree_toolkit-2.0-py2.7.egg\stk_gui\interface.py", line 2297, in on_sub_taxa_sub_taxa_button
  File "C:\Python27\lib\site-packages\supertree_toolkit-2.0-py2.7.egg\stk\supertree_toolkit.py", line 1678, in substitute_taxa
  File "C:\Python27\lib\site-packages\supertree_toolkit-2.0-py2.7.egg\stk\supertree_toolkit.py", line 3265, in _swap_tree_in_XML
ValueError: invalid literal for int() with base 10: 'ASTRAL'

[Jon Hill (jon-hill)]

Hi @moon1996. As above, this bug is caused by assuming tree names in the PHYML. Your tree name should be Author_1, Author_2, etc. If you Author has "_" in it, then swapping that for a "-" or similar should fix this.

Alternatively, grab the latest STK from git hub (link above), which should be fixed.

A python3 version of STK is in the works too.