# FileNotFoundError: \[Errno 2\] No such file or directory: 'bowtie2-build'

**URL:** <https://forum.biobakery.org/t/filenotfounderror-errno-2-no-such-file-or-directory-bowtie2-build/1786>\
**Category:** MetaPhlAn\
**Created:** [March 14, 2021, 4:13pm UTC](https://forum.biobakery.org/t/filenotfounderror-errno-2-no-such-file-or-directory-bowtie2-build/1786 "2021-03-14T16:13:02Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![ryzary](https://avatars.discourse-cdn.com/v4/letter/r/51bf81/32.png) [@ryzary](https://forum.biobakery.org/u/ryzary)\
**Post date:** [March 14, 2021, 4:13pm UTC](https://forum.biobakery.org/t/filenotfounderror-errno-2-no-such-file-or-directory-bowtie2-build/1786/1 "2021-03-14T16:13:02Z")

</div>

Hi, I have installed metaphlan3 using pip.

When I run “metaphlan --install”, I got the following error:

Downloading MetaPhlAn database  
Please note due to the size this might take a few minutes

File /opt/anaconda3/envs/metaphlan3/lib/python3.9/site-packages/metaphlan/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.tar already present!

File /opt/anaconda3/envs/metaphlan3/lib/python3.9/site-packages/metaphlan/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.md5 already present!  
Traceback (most recent call last):  
File “/opt/anaconda3/envs/metaphlan3/bin/metaphlan”, line 8, in   
sys.exit(main())  
File “/opt/anaconda3/envs/metaphlan3/lib/python3.9/site-packages/metaphlan/metaphlan.py”, line 925, in main  
pars[‘index’] = check\_and\_install\_database(pars[‘index’], pars[‘bowtie2db’], pars[‘bowtie2\_build’], pars[‘nproc’], pars[‘force\_download’])  
File “/opt/anaconda3/envs/metaphlan3/lib/python3.9/site-packages/metaphlan/ **init**.py”, line 301, in check\_and\_install\_database  
download\_unpack\_tar(index, bowtie2\_db, bowtie2\_build, nproc, use\_zenodo)  
File “/opt/anaconda3/envs/metaphlan3/lib/python3.9/site-packages/metaphlan/ **init**.py”, line 180, in download\_unpack\_tar  
bt2\_build\_output = subp.check\_output([bowtie2\_build, ‘–usage’], stderr=subp.STDOUT)  
File “/opt/anaconda3/envs/metaphlan3/lib/python3.9/subprocess.py”, line 420, in check\_output  
return run(\*popenargs, stdout=PIPE, timeout=timeout, check=True,  
File “/opt/anaconda3/envs/metaphlan3/lib/python3.9/subprocess.py”, line 501, in run  
with Popen(\*popenargs, \*\*kwargs) as process:  
File “/opt/anaconda3/envs/metaphlan3/lib/python3.9/subprocess.py”, line 947, in **init**  
self.\_execute\_child(args, executable, preexec\_fn, close\_fds,  
File “/opt/anaconda3/envs/metaphlan3/lib/python3.9/subprocess.py”, line 1819, in \_execute\_child  
raise child\_exception\_type(errno\_num, err\_msg, err\_filename)  
**FileNotFoundError: [Errno 2] No such file or directory: 'bowtie2-build’**

---

<div class="post-metadata">

**Author:** ![Heba\_Allah\_Mohamed\_H](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/heba_allah_mohamed_h/32/1733_2.png) [@Heba\_Allah\_Mohamed\_H](https://forum.biobakery.org/u/Heba_Allah_Mohamed_H)\
**Post date:** [December 1, 2022, 4:44pm UTC](https://forum.biobakery.org/t/filenotfounderror-errno-2-no-such-file-or-directory-bowtie2-build/1786/2 "2022-12-01T16:44:11Z")

</div>

Hi , i have the same problem, did u manged to solve it?

 ![image](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/e/e0a98a7c79ba0ba1a4b0054b4aa188f7680b97e8.png)

---

<div class="post-metadata">

**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [December 6, 2022, 8:19am UTC](https://forum.biobakery.org/t/filenotfounderror-errno-2-no-such-file-or-directory-bowtie2-build/1786/3 "2022-12-06T08:19:19Z")

</div>

Hi @ryzary  
Installing metaphlan using pip will not install all the dependecies necesary and you should install them manually. As an alternative, I recommend you to install it using conda