Lefse format data error

Downstream analysis and statistics
1

Hi,

I encountered a data formatting error when running LEfSe on my dataset. To troubleshoot, I tried the sample input data as well, but the same error still occurred. I also tested MaAsLin2 with the sample input data and ran into the same issue there.

Could you please take a look and help investigate? Thanks very much.

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Fatal error: Exit code 1 ()

Traceback (most recent call last):
  File "/galaxy_venv/bin/lefse_format_input.py", line 33, in <module>
    sys.exit(load_entry_point('lefse==1.1.2', 'console_scripts', 'lefse_format_input.py')())
  File "/galaxy_venv/bin/lefse_format_input.py", line 25, in importlib_load_entry_point
    return next(matches).load()
  File "/galaxy_venv/lib/python3.7/site-packages/importlib_metadata/__init__.py", line 96, in load
    module = import_module(match.group('module'))
  File "/tool_deps/_conda/lib/python3.7/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 668, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 638, in _load_backward_compatible
  File "/galaxy_venv/lib/python3.7/site-packages/lefse-1.1.2-py3.7.egg/lefse/lefse_format_input.py", line 7, in <module>
    __requires__ = 'lefse==1.1.2'
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 668, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 638, in _load_backward_compatible
  File "/galaxy_venv/lib/python3.7/site-packages/lefse-1.1.2-py3.7.egg/lefsebiom/AbundanceTable.py", line 54, in <module>
  File "/galaxy_venv/lib/python3.7/site-packages/biom/__init__.py", line 51, in <module>
    from .table import Table
  File "/galaxy_venv/lib/python3.7/site-packages/biom/table.py", line 196, in <module>
    from ._filter import _filter
  File "biom/_filter.pyx", line 1, in init biom._filter
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject
2

Hi,

Would MaAsLin 2 or 3 work for what you’re trying to do? In general we’re moving away from LEfSe and towards more modern methods that have lower false discovery rates.

Will

3

Thank you for your reply. I also tried running MaAsLin 2 on the Galaxy web portal using the sample input, and it produced the same error as LEfSe. This makes me wonder whether it might be a common issue that can be resolved. Thank you!

4

Got it - I’ve forwarded this to the people in the lab who run Galaxy. In the meantime, if you’re comfortable working with R locally, the R versions should work properly.

5

Hi @Yiwei_Sun ,

Would you might attaching/forwarding me your input data that you are using for MaAsLin 2 or LEfSe please and I can look into whats going on with the Galaxy runs?

Regards,
Sagun

6

Hi Sagun,

For LEfSe, I tried using my data and the sample input data (hmp_aerobiosis_small.txt). Both gave me the same set of errors.

For MaAsLin2, I also tried the sample input but it also did not work out on the galaxy web portal.

Could you try running LEfSe and MaAsLin2 using the sample input and see if they work for you? Much appreciated!

Best,

Yiwei

hmp_aerobiosis_small.txt (660.1 KB)