# Bypass prescreen always = True

**URL:** <https://forum.biobakery.org/t/bypass-prescreen-always-true/4939>\
**Category:** HUMAnN\
**Created:** [March 8, 2023, 7:41am UTC](https://forum.biobakery.org/t/bypass-prescreen-always-true/4939 "2023-03-08T07:41:54Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![xiaoafei](https://avatars.discourse-cdn.com/v4/letter/x/2acd7d/32.png) [@xiaoafei](https://forum.biobakery.org/u/xiaoafei)\
**Post date:** [March 8, 2023, 7:41am UTC](https://forum.biobakery.org/t/bypass-prescreen-always-true/4939/1 "2023-03-08T07:41:54Z")

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i have installed humann 3.6.1 by `pip install humann --no-binary :all: -i https://pypi.tuna.tsinghua.edu.cn/simple`, but it always run by  
RUN MODES

```auto
resume = False
verbose = False
bypass prescreen = True
bypass nucleotide index = True
bypass nucleotide search = False
bypass translated search = False
translated search = diamond
threads = 14

```

my code is `humann --input /mnt/qc/MHBA/MHBA1/MHBA1.fastq --output /mnt/gongneng --threads 2 --metaphlan-options="--bowtie2db /mnt/shujuku/humann3/metaphlan --index v30_CHOCOPhlAn_201901" --bypass-nucleotide-index`, and i have set bypass prescreen = False before run humann.

---

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**Author:** ![lauren.j.mciver](https://avatars.discourse-cdn.com/v4/letter/l/f05b48/32.png) [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver)\
**Post date:** [March 15, 2023, 3:27pm UTC](https://forum.biobakery.org/t/bypass-prescreen-always-true/4939/2 "2023-03-15T15:27:23Z")

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Hi, Thank you for the detailed post. If you set --bypass-nucleotide-index it will search for a custom nucleotide database and will set bypass prescreen to True.

Thank you,  
Lauren