# Error running fasta files Metaphlan4.2.3

**URL:** <https://forum.biobakery.org/t/error-running-fasta-files-metaphlan4-2-3/8568>\
**Category:** MetaPhlAn\
**Created:** [October 20, 2025, 5:44pm UTC](https://forum.biobakery.org/t/error-running-fasta-files-metaphlan4-2-3/8568 "2025-10-20T17:44:24Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![dcruze](https://avatars.discourse-cdn.com/v4/letter/d/e36b37/32.png) [@dcruze](https://forum.biobakery.org/u/dcruze)\
**Post date:** [October 20, 2025, 5:44pm UTC](https://forum.biobakery.org/t/error-running-fasta-files-metaphlan4-2-3/8568/1 "2025-10-20T17:44:25Z")

</div>

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

Command:

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

```

Version:

Metaphlan 4.2.3

Error Message:

```auto
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

---

<div class="post-metadata">

**Author:** ![Gaopu](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/gaopu/32/2096_2.png) [@Gaopu](https://forum.biobakery.org/u/Gaopu)\
**Post date:** [October 21, 2025, 8:22am UTC](https://forum.biobakery.org/t/error-running-fasta-files-metaphlan4-2-3/8568/2 "2025-10-21T08:22:09Z")

</div>

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.

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<div class="post-metadata">

**Author:** ![Claudia\_Mengoni](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/claudia_mengoni/32/2871_2.png) [@Claudia\_Mengoni](https://forum.biobakery.org/u/Claudia_Mengoni)\
**Post date:** [October 21, 2025, 8:23am UTC](https://forum.biobakery.org/t/error-running-fasta-files-metaphlan4-2-3/8568/3 "2025-10-21T08:23:31Z")

</div>

Hi,

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

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<div class="post-metadata">

**Author:** ![fconstancias](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fconstancias/32/190_2.png) [@fconstancias](https://forum.biobakery.org/u/fconstancias)\
**Post date:** [October 21, 2025, 6:51pm UTC](https://forum.biobakery.org/t/error-running-fasta-files-metaphlan4-2-3/8568/4 "2025-10-21T18:51:54Z")

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Cool. I have just realize this as well with 4.2.3