# Bowtie2 error in metaphlan3

**URL:** <https://forum.biobakery.org/t/bowtie2-error-in-metaphlan3/3089>\
**Category:** MetaPhlAn\
**Created:** [February 5, 2022, 12:38am UTC](https://forum.biobakery.org/t/bowtie2-error-in-metaphlan3/3089 "2022-02-05T00:38:57Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![khem](https://avatars.discourse-cdn.com/v4/letter/k/6f9a4e/32.png) [@khem](https://forum.biobakery.org/u/khem)\
**Post date:** [February 5, 2022, 12:38am UTC](https://forum.biobakery.org/t/bowtie2-error-in-metaphlan3/3089/1 "2022-02-05T00:38:57Z")

</div>

Hello,  
I am trying to run metaphlan3 but keep getting an error  
i followed some of the old posts like installing libtbb or reinstalling bowtie2 and metaphlan3 etc.  
nothing worked for me

* * *

Traceback (most recent call last):  
File “/home/scebmeta/bin/miniconda3/envs/metaphlan3/bin/metaphlan”, line 10, in  
sys.exit(main())  
File “/home/scebmeta/bin/miniconda3/envs/metaphlan3/lib/python3.7/site-packages/metaphlan/metaphlan.py”, line 1060, in main  
min\_alignment\_len=pars[‘min\_alignment\_len’], read\_min\_len=pars[‘read\_min\_len’], min\_mapq\_val=pars[‘min\_mapq\_val’])  
File “/home/scebmeta/bin/miniconda3/envs/metaphlan3/lib/python3.7/site-packages/metaphlan/metaphlan.py”, line 434, in run\_bowtie2  
nreads, avg\_read\_length = list(map(float, read\_fastx\_stderr[0].decode().split()))  
IndexError: list index out of range

my command was, started only for one sample

bowtie2db="/media/scebmeta/SSD/DB/"  
metaphlan KN100\_R1.unmapped.fastq.gz KN100\_R2.unmapped.fastq.gz --bowtie2db $bowtie2db --bt2\_ps very-sensitive --ignore\_eukaryotes --ignore\_archaea --input\_type fastq -t rel\_ab\_w\_read\_stats --bowtie2out profiled\_very\_sensitive/1x.bowtie2\_out.bz2 --nproc $(nproc) -o profiled\_very\_sensitive/1x.txt  
…  
FYI: installed in a conda environment and downloaded the database in a separate folder  
Please can you help me to solve this issue?  
Thanks,  
Khem