OverflowError when trying passing centrifuge input test

[pimarin]

Hello,

I tried to update the recentrifuge galaxy tool from 1.12.1 to 1.13.1 but when I tested centrifuge input, the tool failed and make and error. Inputs from https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge/test-data

• test-db is a light taxa database
• centrifuge folder contain workging files with 1.12 version Command used : rcf -n ./test-data/test-db -f rcf_test/centrifuge_1.out

Output observed :

=-= /opt/conda/envs/recentrifuge/bin/rcf =-= v1.13.1 - Jan 2024 =-= by Jose Manuel Martí =-=

Loading NCBI nodes... OK! 
Loading NCBI names... OK! 
Building dict of parent to children taxa... OK! 

Please, wait, processing files in parallel...

multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/opt/conda/envs/recentrifuge/lib/python3.11/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
                    ^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/recentrifuge/lib/python3.11/site-packages/recentrifuge/taxclass.py", line 128, in process_output
    tree.allin1(ontology=ontology, counts=counts, scores=scores,
  File "/opt/conda/envs/recentrifuge/lib/python3.11/site-packages/recentrifuge/trees.py", line 276, in allin1
    child_acc: Union[int, None] = self[tid].allin1(
                                  ^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/recentrifuge/lib/python3.11/site-packages/recentrifuge/trees.py", line 276, in allin1
    child_acc: Union[int, None] = self[tid].allin1(
                                  ^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/recentrifuge/lib/python3.11/site-packages/recentrifuge/trees.py", line 276, in allin1
    child_acc: Union[int, None] = self[tid].allin1(
                                  ^^^^^^^^^^^^^^^^^
  [Previous line repeated 3 more times]
  File "/opt/conda/envs/recentrifuge/lib/python3.11/site-packages/recentrifuge/trees.py", line 305, in allin1
    update_score_and_acc(chld, child_acc)
  File "/opt/conda/envs/recentrifuge/lib/python3.11/site-packages/recentrifuge/trees.py", line 268, in update_score_and_acc
    self[tid].score = swmean(
                      ^^^^^^^
  File "/opt/conda/envs/recentrifuge/lib/python3.11/site-packages/recentrifuge/trees.py", line 263, in swmean
    (cnt1 * 10**sco1 + cnt2 * 10**sco2) / (cnt1 + cnt2)
            ~~^^~~~~
OverflowError: (34, 'Numerical result out of range')
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/opt/conda/envs/recentrifuge/bin/rcf", line 928, in <module>
    main()
  File "/opt/conda/envs/recentrifuge/bin/rcf", line 887, in main
    read_samples()
  File "/opt/conda/envs/recentrifuge/bin/rcf", line 492, in read_samples
    input_files, [r.get() for r in async_results]):
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/recentrifuge/bin/rcf", line 492, in <listcomp>
    input_files, [r.get() for r in async_results]):
                  ^^^^^^^
  File "/opt/conda/envs/recentrifuge/lib/python3.11/multiprocessing/pool.py", line 774, in get
    raise self._value
OverflowError: (34, 'Numerical result out of range')

[khyox]

Hi @pimarin and thank you for the bug report. Just the day before your report, I issued Recentrifuge v1.13.2, which should address this bug introduced in v1.13.0. I hope it quickly made its way to galaxy and you can see this solved now. Please feel free to reopen if you still see that after upgrading to v1.13.2. Thanks!

[pimarin]

Thank you @khyox !

[khyox]

You're welcome @pimarin, and thanks again for reporting the issue! :)