jeetsukumaran / delineate Goto Github PK

Hi Jeet,
I'm trying to use DELINEATE with an empirical dataset, but I'm getting different errors, and cannot figure out why.

(1) First, there seem to be a syntax error in the control.py ?
I got this error:

delineate-estimate partitions -t starbeast.nex --t Imap.txt
Traceback (most recent call last):
File "/usr/local/bin/delineate-estimate", line 41, in
from delineate import control
File "/Library/Python/2.7/site-packages/delineate/control.py", line 343
**self._logger_kwargs,
^
SyntaxError: invalid syntax

The error doesn't show up any more after I removed the line 343 from control.py: **self._logger_kwargs,
I believe the ** intended to be a comment?
BUT, I'm not sure if by deleting this line, something is going to be problematic later.

(2) Now the program is starting, but I get a new error with treemodel.py, and I couldn't figure out why this is happening. Note that I get this same error if I use a nexus tree in data/speciation-completion-rate/s1-298db43

delineate-estimate partitions -t starbeast.nex --t Imap.txt

[delineate-estimate 2020-02-14 12:54:51] 19 lineages found on population tree:
[ 1/19 ] 'Apoast'
[ 2/19 ] 'Apocha'
[ 3/19 ] 'Aposup'
[ 4/19 ] 'Apofla'
[ 5/19 ] 'Apoglo'
[ 6/19 ] 'Apozal'
[ 7/19 ] 'AsLcit'
[ 8/19 ] 'AsMtol'
[ 9/19 ] 'Tsccit'
[ 10/19 ] 'Ayecit'
[ 11/19 ] 'Xilama'
[ 12/19 ] 'Xilsag'
[ 13/19 ] 'Xilxil'
[ 14/19 ] 'Xilvir'
[ 15/19 ] 'Mancit'
[ 16/19 ] 'Manlab'
[ 17/19 ] 'Mascit'
[ 18/19 ] 'Niccit'
[ 19/19 ] 'Niclab'
[delineate-estimate 2020-02-14 12:54:51] 19 lineages found in configuration file fully concordant with tree lineages
[delineate-estimate 2020-02-14 12:54:51] 15 species defined in configuration constraints, with 15 lineages assigned:
[ 1/15 ] 'Apoast' (1 lineages)
[ 2/15 ] 'Apocha' (1 lineages)
[ 3/15 ] 'Apofla' (1 lineages)
[ 4/15 ] 'Apoglo' (1 lineages)
[ 5/15 ] 'Aposup' (1 lineages)
[ 6/15 ] 'Apozal' (1 lineages)
[ 7/15 ] 'AsLcit' (1 lineages)
[ 8/15 ] 'AsMtol' (1 lineages)
[ 9/15 ] 'Ayecit' (1 lineages)
[ 10/15 ] 'Mascit' (1 lineages)
[ 11/15 ] 'Tsccit' (1 lineages)
[ 12/15 ] 'Xilama' (1 lineages)
[ 13/15 ] 'Xilsag' (1 lineages)
[ 14/15 ] 'Xilvir' (1 lineages)
[ 15/15 ] 'Xilxil' (1 lineages)
[delineate-estimate 2020-02-14 12:54:51] 15 out of 19 lineages assigned by constraints to 15 species:
[ 1/15 ] 'Apoast' (SPECIES: 'Apoast')
[ 2/15 ] 'Apocha' (SPECIES: 'Apocha')
[ 3/15 ] 'Apofla' (SPECIES: 'Apofla')
[ 4/15 ] 'Apoglo' (SPECIES: 'Apoglo')
[ 5/15 ] 'Aposup' (SPECIES: 'Aposup')
[ 6/15 ] 'Apozal' (SPECIES: 'Apozal')
[ 7/15 ] 'AsLcit' (SPECIES: 'AsLcit')
[ 8/15 ] 'AsMtol' (SPECIES: 'AsMtol')
[ 9/15 ] 'Ayecit' (SPECIES: 'Ayecit')
[ 10/15 ] 'Mascit' (SPECIES: 'Mascit')
[ 11/15 ] 'Tsccit' (SPECIES: 'Tsccit')
[ 12/15 ] 'Xilama' (SPECIES: 'Xilama')
[ 13/15 ] 'Xilsag' (SPECIES: 'Xilsag')
[ 14/15 ] 'Xilvir' (SPECIES: 'Xilvir')
[ 15/15 ] 'Xilxil' (SPECIES: 'Xilxil')
[delineate-estimate 2020-02-14 12:54:51] 4 out of 19 lineages not constrained by species assignments:
[ 1/4 ] 'Mancit'
[ 2/4 ] 'Manlab'
[ 3/4 ] 'Niccit'
[ 4/4 ] 'Niclab'
Traceback (most recent call last):
File "delineate-estimate", line 498, in
main()
File "delineate-estimate", line 490, in main
args.func(args=args)
File "delineate-estimate", line 61, in execute_species_partition_estimation
labels=controller.constrained_lineage_leaf_labels)
File "/Library/Python/2.7/site-packages/dendropy/datamodel/treemodel.py", line 3533, in extract_tree_with_taxa_labels
is_apply_filter_to_internal_nodes=False,
File "/Library/Python/2.7/site-packages/dendropy/datamodel/treemodel.py", line 3404, in extract_tree
node_factory=node_factory,
File "/Library/Python/2.7/site-packages/dendropy/datamodel/treemodel.py", line 2267, in extract_subtree
nd1 = node_factory()
TypeError: init() takes exactly 2 arguments (1 given)
dhcp-m08-12:bin melisaolave$ python delineate-estimate partitions --tree-file starbeast-timeCalibrated.nex --config-file Imap.txt
[delineate-estimate 2020-02-14 12:57:21] 19 lineages found on population tree:
[ 1/19 ] 'Apoast'
[ 2/19 ] 'Apocha'
[ 3/19 ] 'Apofla'
[ 4/19 ] 'Apoglo'
[ 5/19 ] 'Aposup'
[ 6/19 ] 'Apozal'
[ 7/19 ] 'AsLcit'
[ 8/19 ] 'AsMtol'
[ 9/19 ] 'Ayecit'
[ 10/19 ] 'Mancit'
[ 11/19 ] 'Manlab'
[ 12/19 ] 'Mascit'
[ 13/19 ] 'Niccit'
[ 14/19 ] 'Niclab'
[ 15/19 ] 'Tsccit'
[ 16/19 ] 'Xilama'
[ 17/19 ] 'Xilsag'
[ 18/19 ] 'Xilvir'
[ 19/19 ] 'Xilxil'
[delineate-estimate 2020-02-14 12:57:21] 19 lineages found in configuration file fully concordant with tree lineages
[delineate-estimate 2020-02-14 12:57:21] 15 species defined in configuration constraints, with 15 lineages assigned:
[ 1/15 ] 'Apoast' (1 lineages)
[ 2/15 ] 'Apocha' (1 lineages)
[ 3/15 ] 'Apofla' (1 lineages)
[ 4/15 ] 'Apoglo' (1 lineages)
[ 5/15 ] 'Aposup' (1 lineages)
[ 6/15 ] 'Apozal' (1 lineages)
[ 7/15 ] 'AsLcit' (1 lineages)
[ 8/15 ] 'AsMtol' (1 lineages)
[ 9/15 ] 'Ayecit' (1 lineages)
[ 10/15 ] 'Mascit' (1 lineages)
[ 11/15 ] 'Tsccit' (1 lineages)
[ 12/15 ] 'Xilama' (1 lineages)
[ 13/15 ] 'Xilsag' (1 lineages)
[ 14/15 ] 'Xilvir' (1 lineages)
[ 15/15 ] 'Xilxil' (1 lineages)
[delineate-estimate 2020-02-14 12:57:21] 15 out of 19 lineages assigned by constraints to 15 species:
[ 1/15 ] 'Apoast' (SPECIES: 'Apoast')
[ 2/15 ] 'Apocha' (SPECIES: 'Apocha')
[ 3/15 ] 'Apofla' (SPECIES: 'Apofla')
[ 4/15 ] 'Apoglo' (SPECIES: 'Apoglo')
[ 5/15 ] 'Aposup' (SPECIES: 'Aposup')
[ 6/15 ] 'Apozal' (SPECIES: 'Apozal')
[ 7/15 ] 'AsLcit' (SPECIES: 'AsLcit')
[ 8/15 ] 'AsMtol' (SPECIES: 'AsMtol')
[ 9/15 ] 'Ayecit' (SPECIES: 'Ayecit')
[ 10/15 ] 'Mascit' (SPECIES: 'Mascit')
[ 11/15 ] 'Tsccit' (SPECIES: 'Tsccit')
[ 12/15 ] 'Xilama' (SPECIES: 'Xilama')
[ 13/15 ] 'Xilsag' (SPECIES: 'Xilsag')
[ 14/15 ] 'Xilvir' (SPECIES: 'Xilvir')
[ 15/15 ] 'Xilxil' (SPECIES: 'Xilxil')
[delineate-estimate 2020-02-14 12:57:21] 4 out of 19 lineages not constrained by species assignments:
[ 1/4 ] 'Mancit'
[ 2/4 ] 'Manlab'
[ 3/4 ] 'Niccit'
[ 4/4 ] 'Niclab'
Traceback (most recent call last):
File "delineate-estimate", line 498, in
main()
File "delineate-estimate", line 490, in main
args.func(args=args)
File "delineate-estimate", line 61, in execute_species_partition_estimation
labels=controller.constrained_lineage_leaf_labels)
File "/Library/Python/2.7/site-packages/dendropy/datamodel/treemodel.py", line 3533, in extract_tree_with_taxa_labels
is_apply_filter_to_internal_nodes=False,
File "/Library/Python/2.7/site-packages/dendropy/datamodel/treemodel.py", line 3404, in extract_tree
node_factory=node_factory,
File "/Library/Python/2.7/site-packages/dendropy/datamodel/treemodel.py", line 2267, in extract_subtree
nd1 = node_factory()
TypeError: init() takes exactly 2 arguments (1 given)

Thanks for your help!

Melisa