# Humann can not run with metaphlan together

**URL:** https://forum.biobakery.org/t/humann-can-not-run-with-metaphlan-together/774
**Category:** HUMAnN
**Created:** [July 26, 2020, 1:08pm UTC](https://forum.biobakery.org/t/humann-can-not-run-with-metaphlan-together/774 "2020-07-26T13:08:33Z")
**Posts on this page:** 1
**Showing post:** 7

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### Author: ![wenping](https://avatars.discourse-cdn.com/v4/letter/w/e56c9b/32.png) [@wenping](https://forum.biobakery.org/u/wenping)
#### Post date: [July 29, 2020, 8:27am UTC](https://forum.biobakery.org/t/humann-can-not-run-with-metaphlan-together/774/7 "2020-07-29T08:27:55Z")

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Hi Francesco,  
I run the following code, but it doesn’t work:

(py37) [zhangwenping@localhost try\_humann]$ humann --input /data/liying\_metagenome/clean\_data\_liying/SRR5130527\_paired.1.fastq --output try\_SRR5130527\_paired.1 --metaphlan-options -x mpa\_v30\_CHOCOPhlAn\_201901 --bowtie2db /data/xmjd/miniconda2/envs/py37/lib/python3.7/site-packages/metaphlan/metaphlan\_databases/  
usage: humann [-h] [–version] [-v] [-r] [–bypass-prescreen]  
[–bypass-nucleotide-index] [–bypass-translated-search]  
[–bypass-nucleotide-search] -i \<input.fastq\> -o   
[–nucleotide-database \<nucleotide\_database\>]  
[–annotation-gene-index \<3\>]  
[–protein-database \<protein\_database\>] [–evalue \<1.0\>]  
[–search-mode {uniref50,uniref90}] [–metaphlan]  
[–metaphlan-options \<metaphlan\_options\>]  
[–diamond-options \<diamond\_options\>]  
[–bowtie-options \<bowtie\_options\>] [–o-log \<sample.log\>]  
[–log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}]  
[–remove-temp-output] [–threads \<1\>]  
[–prescreen-threshold \<0.01\>]  
[–nucleotide-identity-threshold \<0.0\>]  
[–translated-identity-threshold \<Automatically: 50.0 or 80.0, Custom: 0.0-100.0\>]  
[–translated-subject-coverage-threshold \<50.0\>]  
[–nucleotide-subject-coverage-threshold \<50.0\>]  
[–translated-query-coverage-threshold \<90.0\>]  
[–nucleotide-query-coverage-threshold \<90.0\>]  
[–bowtie2] [–usearch]  
[–rapsearch] [–diamond]  
[–taxonomic-profile \<taxonomic\_profile.tsv\>]  
[–id-mapping \<id\_mapping.tsv\>]  
[–translated-alignment {usearch,rapsearch,diamond}]  
[–xipe {on,off}] [–minpath {on,off}] [–pick-frames {on,off}]  
[–gap-fill {on,off}] [–output-format {tsv,biom}]  
[–output-max-decimals \<10\>] [–output-basename \<sample\_name\>]  
[–remove-stratified-output]  
[–remove-column-description-output]  
[–input-format {fastq,fastq.gz,fasta,fasta.gz,sam,bam,blastm8,genetable,biom}]  
[–pathways-database \<pathways\_database.tsv\>]  
[–pathways {metacyc,unipathway}]  
[–memory-use {minimum,maximum}]  
humann: error: argument --metaphlan-options: expected one argument

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