IndexError: list index out of range

[StepanSaenko]

Hello! I tried with different files and everytime got this:

File "/home/saenkos/anaconda3/envs/myenv/bin/omark", line 4, in <module>
    __import__('pkg_resources').run_script('omark==0.2.6', 'omark')
  File "/home/saenkos/anaconda3/envs/myenv/lib/python3.11/site-packages/pkg_resources/__init__.py", line 720, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/home/saenkos/anaconda3/envs/myenv/lib/python3.11/site-packages/pkg_resources/__init__.py", line 1570, in run_script
    exec(script_code, namespace, namespace)
  File "/home/saenkos/anaconda3/envs/myenv/lib/python3.11/site-packages/omark-0.2.6-py3.11.egg/EGG-INFO/scripts/omark", line 45, in <module>
  File "/home/saenkos/anaconda3/envs/myenv/lib/python3.11/site-packages/omark-0.2.6-py3.11.egg/omark/omark.py", line 183, in launcher
  File "/home/saenkos/anaconda3/envs/myenv/lib/python3.11/site-packages/omark-0.2.6-py3.11.egg/omark/omark.py", line 65, in get_omamer_qscore
  File "/home/saenkos/anaconda3/envs/myenv/lib/python3.11/site-packages/omark-0.2.6-py3.11.egg/omark/species_determination.py", line 54, in get_present_lineages
  File "/home/saenkos/anaconda3/envs/myenv/lib/python3.11/site-packages/omark-0.2.6-py3.11.egg/omark/species_determination.py", line 102, in tree_from_taxlist
IndexError: list index out of range
Closing remaining open files:../../LUCA.h5...done

Could you please help me, what am I doing wrong?

[YanNevers]

Hello @StepanSaenko ,

Thanks for letting us know about your issue. I'll investigate and try to solve this ASAP.

Could you let me know what was the command line you used when having this error. Is it also possible for you to share one of the input omamer files you were using? It could be helpful for me to replicate this error.

[StepanSaenko]

@YanNevers thank you for your reply. Unfortunately, I cannot reproduce this error. I created a new conda environment, then reinstalled OMArk and everything was fine.

Sorry for disturbing you.