Error running fasta files Metaphlan4.2.3

Microbial community profiling MetaPhlAn
1

Getting error when trying to run the test file Supragingival_plaque.fasta. from documentation, works fine with fastq.gz format

Command:

metaphlan --nproc 8 --input_type fasta SRS014476-Supragingival_plaque.fasta.gz –output_file profile_t.txt

Version:

Metaphlan 4.2.3

Error Message:

Traceback (most recent call last):
  File "/home//.pixi/envs/mpa4/bin/metaphlan", line 10, in <module>
    sys.exit(main())
             ~~~~^^
  File "/home//.pixi/envs/mpa4/lib/python3.13/site-packages/metaphlan/metaphlan.py", line 2342, in main
    metaphlan_runner.run_metaphlan()
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
  File "/home//.pixi/envs/mpa4/lib/python3.13/site-packages/metaphlan/metaphlan.py", line 1943, in run_metaphlan
    self.metaphlan_analysis.report_results(self.tree, self.total_metagenome, self.avg_read_length)
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home//.pixi/envs/mpa4/lib/python3.13/site-packages/metaphlan/metaphlan.py", line 1409, in report_results
    self.get_mapped_fraction()
    ~~~~~~~~~~~~~~~~~~~~~~~~^^
  File "/home//.pixi/envs/mpa4/lib/python3.13/site-packages/metaphlan/metaphlan.py", line 1292, in get_mapped_fraction
    self.mapped = self.tree.relative_abundances()
                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
  File "/home//.pixi/envs/mpa4/lib/python3.13/site-packages/metaphlan/metaphlan.py", line 339, in relative_abundances
    rounding_value = conditional_rounding(all_rel_ab)
                     ^^^^^^^^^^^^^^^^^^^^
NameError: name 'conditional_rounding' is not defined. Did you mean: 'self.conditional_rounding'?

Environment:

pixi

Any help will be appreciated

2

I’ve also met the same error with metaphlan4.2.3 for both fastq and fasta files. It seems to be a 4.2.3 version-specific problem, since analyses of fastq and fasta files are always OK with the 4.2.2 version.

3

Hi,

Yes it is an issue with 4.2.3. I am now pushing a fix as 4.2.4, sorry for the inconvenience

2 Likes
4

Cool. I have just realize this as well with 4.2.3