# Trouble with Arguments and Time it Takes to Make Tree

**URL:** <https://forum.biobakery.org/t/trouble-with-arguments-and-time-it-takes-to-make-tree/7861>\
**Category:** PhyloPhlAn\
**Created:** [February 24, 2025, 5:36pm UTC](https://forum.biobakery.org/t/trouble-with-arguments-and-time-it-takes-to-make-tree/7861 "2025-02-24T17:36:36Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Alex-A-B-C](https://avatars.discourse-cdn.com/v4/letter/a/b9e5f3/32.png) [@Alex-A-B-C](https://forum.biobakery.org/u/Alex-A-B-C)\
**Post date:** [February 24, 2025, 5:36pm UTC](https://forum.biobakery.org/t/trouble-with-arguments-and-time-it-takes-to-make-tree/7861/1 "2025-02-24T17:36:36Z")

</div>

Hello, I recently started using PhyloPhlAn. I have 500 strains of interest that I want to make the tree with. To do so I uploaded the nucelotide WGS sequences for them, and ran PhyloPhlAn.

```auto
phylophlan \
    -i key_genomes\
    -d phylophlan \
    -f supertree_aa.cfg \
    --force_nucleotides \
    --diversity high \
    --accurate \
    -o phylophlan_output\
    --nproc 32\
    --verbose \
    --maas phylophlan.tsv
    2>&1 | tee logs/phylophlan.log

```

I added the --maas as troubleshooting board reccomended this. It is now day 3 and lines are being generated with different versions of this

`"Refining gene tree "phylophlan key_genomes/tmp/trim_not_variant/p0318.aln" "p0101.tre" generated in 9444s"`

I have two major concerns:

**1. Did I specify the right arguments given that I have 500 nucleotide genomes?** If not what corrections do I need, I kept on getting errors until I used the above code. I recognzie PhyloPhlAn tends to take in a proteomic upload, so its this the cause of the issue?  
**2. Is the 3-4 days time window to be expected?** I’m concerned about it running for a while on errenous arguments and that’s why it’s taking so long, I have 32CPU dedciated per the code for refernece.