# HUMAnN Parameters not work for bowtie2 and diamond

**URL:** https://forum.biobakery.org/t/humann-parameters-not-work-for-bowtie2-and-diamond/7081
**Category:** HUMAnN
**Created:** [May 23, 2024, 6:14am UTC](https://forum.biobakery.org/t/humann-parameters-not-work-for-bowtie2-and-diamond/7081 "2024-05-23T06:14:53Z")
**Posts on this page:** 2
**Page:** 1

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### Author: ![BaylorLyu](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/baylorlyu/32/2865_2.png) [@BaylorLyu](https://forum.biobakery.org/u/BaylorLyu)
#### Post date: [May 23, 2024, 6:14am UTC](https://forum.biobakery.org/t/humann-parameters-not-work-for-bowtie2-and-diamond/7081/1 "2024-05-23T06:14:53Z")

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hello there,  
I submitted a test work for humann:  
humann --input-format fastq clean/test.fastq   
–taxonomic-profile metaphlan/test.txt   
–output temp/humann --threads 8   
–bowtie2-options “–fast” --diamond-options “–fast” \   
–metaphlan-options ’ $db --index mpa\_vJun23\_CHOCOPhlAnSGB\_202307 --offline’

but humann did work with parameters "–bowtie2-options “–fast” --diamond-options “–fast” ,how to fix it ?

error:  
usage: humann [-h] -i \<input.fastq\> -o [–threads \<1\>] [–version] [-r] [–bypass-nucleotide-index] [–bypass-nucleotide-search] [–bypass-prescreen] [–bypass-translated-search] [–taxonomic-profile \<taxonomic\_profile.tsv\>]  
[–memory-use {minimum,maximum}] [–input-format {fastq,fastq.gz,fasta,fasta.gz,sam,bam,blastm8,genetable,biom}] [–search-mode {uniref50,uniref90}] [-v] [–metaphlan] [–metaphlan-options \<metaphlan\_options\>]  
[–prescreen-threshold \<0.01\>] [–bowtie2] [–bowtie-options \<bowtie\_options\>] [–nucleotide-database \<nucleotide\_database\>] [–nucleotide-identity-threshold \<0.0\>] [–nucleotide-query-coverage-threshold \<90.0\>]  
[–nucleotide-subject-coverage-threshold \<50.0\>] [–diamond] [–diamond-options \<diamond\_options\>] [–evalue \<1.0\>] [–protein-database \<protein\_database\>] [–rapsearch]  
[–translated-alignment {usearch,rapsearch,diamond}] [–translated-identity-threshold \<Automatically: 50.0 or 80.0, Custom: 0.0-100.0\>] [–translated-query-coverage-threshold \<90.0\>]  
[–translated-subject-coverage-threshold \<50.0\>] [–usearch] [–gap-fill {on,off}] [–minpath {on,off}] [–pathways {metacyc,unipathway}] [–pathways-database \<pathways\_database.tsv\>] [–xipe {on,off}]  
[–annotation-gene-index \<3\>] [–id-mapping \<id\_mapping.tsv\>] [–remove-temp-output] [–log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [–o-log \<sample.log\>] [–output-basename \<sample\_name\>] [–output-format {tsv,biom}]  
[–output-max-decimals \<10\>] [–remove-column-description-output] [–remove-stratified-output]  
humann: error: argument --diamond-options: expected one argument

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<div class="post-metadata">

### Author: ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)
#### Post date: [June 20, 2024, 9:09pm UTC](https://forum.biobakery.org/t/humann-parameters-not-work-for-bowtie2-and-diamond/7081/2 "2024-06-20T21:09:40Z")

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When specifying DIAMOND options you still need to include the default settings that HUMAnN requires, namely the output formatting. Here is a sample custom command I’ve used as an example:

`--diamond-options` ` "--top 1 --outfmt 6 --sensitive"`

I also note that you have some long dashes (rather than `-`s) in the code you pasted. That might also lead to problems.