issue with 'NoneType' object, no attribute 'get_newick_repr'

FePhyFoFum / phlawd_db_editor

edit the databases used for pyphlawd

GNU General Public License v3.0

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issue with 'NoneType' object, no attribute 'get_newick_repr' #6

Open mlatvis opened 3 years ago

mlatvis commented 3 years ago

STARTING PYPHLAWD ╰(‘ω’ )╯ LIMITING TO TAXA IN taxalist MAKING TREE Angiosperms "҉( ‘ω’ )/҉ Traceback (most recent call last): File "/gpfs/shared/apps_local/PyPHLAWD/src/get_ncbi_tax_tree_no_species.py", line 98, in print(tree.get_newick_repr(False)+";") AttributeError: 'NoneType' object has no attribute 'get_newick_repr' Traceback (most recent call last): File "/gpfs/shared/apps_local/PyPHLAWD/src/setup_clade.py", line 43, in trn = tree_reader.read_tree_file_iter(tname).next().label StopIteration

Cactusolo commented 11 months ago

Hi @mlatvis ,

Have you fixed this issue? I saw some discussion in #2 , but still not helpful --- I got new error with phlawd_db_editor.py, when I want to check if the clad exist.

python phlawd_db_editor.py -i Pinus -b ../../Projects/PHLAWD_DBS/pln.2023.db opening logfile phlawd_db_editor.log connecting to ../../Projects/PHLAWD_DBS/pln.2023.db

and the log file says: Tue, 26 Sep 2023 15:15:13 || creating the phlawd_db_editor_newids table with start value 66600001