# Error with bowtie2-build when running humann3

**URL:** <https://forum.biobakery.org/t/error-with-bowtie2-build-when-running-humann3/6430>\
**Category:** HUMAnN\
**Created:** [January 8, 2024, 9:23pm UTC](https://forum.biobakery.org/t/error-with-bowtie2-build-when-running-humann3/6430 "2024-01-08T21:23:17Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Chris](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/chris/32/2640_2.png) [@Chris](https://forum.biobakery.org/u/Chris)\
**Post date:** [January 8, 2024, 9:23pm UTC](https://forum.biobakery.org/t/error-with-bowtie2-build-when-running-humann3/6430/1 "2024-01-08T21:23:17Z")

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Hi community,

I recently get the error with the following error when running Humann3:

**Total species selected from prescreen: 674**

**Selected species explain 99.66% of predicted community composition**

**Creating custom ChocoPhlAn database …**

**Running bowtie2-build …**

**CRITICAL ERROR: Error executing: …**

I try many times but still not solve this problem.  
The last try was, I installed metaphlan4 first, and installed humann3, and run metaphlan4, there is no error.  
But this error was obtained when I run humann3.

humann v3.8  
MetaPhlAn version 4.0.6 (1 Mar 2023)  
bowtie2 version:  
miniconda3/envs/humann3/bin/bowtie2-align-s version 2.5.1  
64-bit  
Built on fv-az456-736  
Tue Jan 31 03:03:11 UTC 2023  
Compiler: gcc version 10.4.0 (conda-forge gcc 10.4.0-19)  
Options: -O3 -msse2 -funroll-loops -g3 -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/qli/miniconda3/envs/humann3/include -fdebug-prefix-map=/opt/conda/conda-bld/bowtie2\_1675132819676/work=/usr/local/src/conda/bowtie2-2.5.1 -fdebug-prefix-map=/home/qli/miniconda3/envs/humann3=/usr/local/src/conda-prefix -std=c++11 -DPOPCNT\_CAPABILITY -DNO\_SPINLOCK -DWITH\_QUEUELOCK=1 -DWITH\_ZSTD  
Sizeof {int, long, long long, void\*, size\_t, off\_t}: {4, 8, 8, 8, 8, 8}

The command for humann3 is:  
humann --metaphlan-options “–index mpa\_vOct22\_CHOCOPhlAnSGB\_202212 --bowtie2db #the folder” --input-format fastq --input sample.fastq --output humann3\_out --memory-use maximum

Does anyone have ideas? Thanks for your time in advance.

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<div class="post-metadata">

**Author:** ![Chris](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/chris/32/2640_2.png) [@Chris](https://forum.biobakery.org/u/Chris)\
**Post date:** [January 8, 2024, 9:53pm UTC](https://forum.biobakery.org/t/error-with-bowtie2-build-when-running-humann3/6430/2 "2024-01-08T21:53:06Z")

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Full error is:

CRITICAL ERROR: Error executing: /home/qli/miniconda3/envs/humann3/bin/bowtie2-build -f /run/user/1001/gvfs/smb-share:server=lab-dna.local,share=%20lab/humann3\_out/1008C1\_humann\_temp/1008C1\_custom\_chocophlan\_database.ffn /run/user/1001/gvfs/smb-share:server=lab-dna.local,share=%20lab/humann3\_out/1008C1\_humann\_temp/1008C1\_bowtie2\_index

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<div class="post-metadata">

**Author:** ![Chris](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/chris/32/2640_2.png) [@Chris](https://forum.biobakery.org/u/Chris)\
**Post date:** [January 9, 2024, 7:04pm UTC](https://forum.biobakery.org/t/error-with-bowtie2-build-when-running-humann3/6430/3 "2024-01-09T19:04:52Z")

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OK, I think the problem is metaphlan cannot call the files from the share folder. The input files for the bowtie2-build is generated in the same share folder (because I set the --output to the share folder), even if I can access from my own computer. I run in my local computer, and it seems worked : )

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**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:** [January 12, 2024, 10:13pm UTC](https://forum.biobakery.org/t/error-with-bowtie2-build-when-running-humann3/6430/4 "2024-01-12T22:13:57Z")

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Glad you were able to figure it out!