# Metaphlan3 installation fails

**URL:** <https://forum.biobakery.org/t/metaphlan3-installation-fails/350>\
**Category:** MetaPhlAn\
**Created:** [April 18, 2020, 4:56am UTC](https://forum.biobakery.org/t/metaphlan3-installation-fails/350 "2020-04-18T04:56:52Z")\
**Posts on this page:** 20\
**Page:** 1

<div class="post-metadata">

**Author:** ![Andrei\_Prodan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/andrei_prodan/32/66_2.png) [@Andrei\_Prodan](https://forum.biobakery.org/u/Andrei_Prodan)\
**Post date:** [April 18, 2020, 4:56am UTC](https://forum.biobakery.org/t/metaphlan3-installation-fails/350/1 "2020-04-18T04:56:52Z")

</div>

Hi,

I tried to install the new metaphlan3 for testing, but having some trouble. Conda installation installs, but the ‘metaphlan --install’ command fails with the error:

File /home/user/miniconda3/envs/metaphlan/lib/python3.6/site-packages/metaphlan/metaphlan\_databases/file\_list.txt already present!  
Traceback (most recent call last):  
File “/home/user/miniconda3/envs/metaphlan/bin/metaphlan”, line 10, in   
sys.exit(main())  
File “/home/user/miniconda3/envs/metaphlan/lib/python3.6/site-packages/metaphlan/metaphlan.py”, line 1187, in main  
pars[‘index’] = check\_and\_install\_database(pars[‘index’], pars[‘bowtie2db’], pars[‘bowtie2\_build’], pars[‘nproc’], pars[‘force\_download’])  
File “/home/user/miniconda3/envs/metaphlan/lib/python3.6/site-packages/metaphlan/metaphlan.py”, line 610, in check\_and\_install\_database  
download\_unpack\_tar(FILE\_LIST, index, bowtie2\_db, bowtie2\_build, nproc)  
File “/home/user/miniconda3/envs/metaphlan/lib/python3.6/site-packages/metaphlan/metaphlan.py”, line 463, in download\_unpack\_tar  
url\_tar\_file = ls\_f[“mpa\_” + download\_file\_name + “.tar”]  
KeyError: ‘mpa\_mpa\_v296\_CHOCOPhlAn\_201901.tar’

The docker installation (‘sudo docker pull [quay.io/biocontainers/metaphlan](http://quay.io/biocontainers/metaphlan)’) also fails to install with:

Error response from daemon: manifest for [quay.io/biocontainers/metaphlan:latest](http://quay.io/biocontainers/metaphlan:latest) not found: manifest unknown: manifest unknown

---

<div class="post-metadata">

**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\
**Post date:** [April 18, 2020, 6:00pm UTC](https://forum.biobakery.org/t/metaphlan3-installation-fails/350/2 "2020-04-18T18:00:32Z")

</div>

Hi,

Can you please check which build version conda installed?

You can do this by running ‘conda list’ from the activated environment.

I’m already aware of the Docker issue, but it seems a Bioconda issue.

---

<div class="post-metadata">

**Author:** ![Andrei\_Prodan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/andrei_prodan/32/66_2.png) [@Andrei\_Prodan](https://forum.biobakery.org/u/Andrei_Prodan)\
**Post date:** [April 19, 2020, 11:11am UTC](https://forum.biobakery.org/t/metaphlan3-installation-fails/350/3 "2020-04-19T11:11:14Z")

</div>

the metaphalan3 version installed by conda is:

“bioconda/noarch::metaphlan-3.0-pyh5ca1d4c\_1”

---

<div class="post-metadata">

**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\
**Post date:** [April 20, 2020, 9:57am UTC](https://forum.biobakery.org/t/metaphlan3-installation-fails/350/4 "2020-04-20T09:57:00Z")

</div>

It seems that conda is not installing the latest build (pyh5ca1d4c\_2), do you have your conda installation updated and correctly configured to fetch packages from Bioconda? You should have added the channels in the order that is written [here](https://bioconda.github.io/user/install.html#set-up-channels), so the dependecies can be fetched correctly

It seems that the Docker image can be fetched by using this command `docker pull quay.io/biocontainers/metaphlan:3.0--pyh5ca1d4c_2`, I’ve provided to update the documentation

---

<div class="post-metadata">

**Author:** ![Andrei\_Prodan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/andrei_prodan/32/66_2.png) [@Andrei\_Prodan](https://forum.biobakery.org/u/Andrei_Prodan)\
**Post date:** [April 20, 2020, 10:18am UTC](https://forum.biobakery.org/t/metaphlan3-installation-fails/350/5 "2020-04-20T10:18:30Z")

</div>

My mistake! Indeed the conda channel priority wasn’t properly set on my laptop. Now the correct metaphlan version installs (MetaPhlAn version 3.0 (20 Mar 2020) / metaphlan-3.0-pyh5ca1d4c\_2) and the database download works!

---

<div class="post-metadata">

**Author:** ![dkarig](https://avatars.discourse-cdn.com/v4/letter/d/51bf81/32.png) [@dkarig](https://forum.biobakery.org/u/dkarig)\
**Post date:** [May 24, 2020, 3:26pm UTC](https://forum.biobakery.org/t/metaphlan3-installation-fails/350/6 "2020-05-24T15:26:53Z")

</div>

I’m having this issue as well, but I’m having trouble resolving it. It seems that I’m stuck with pyh5ca1d4c\_1 as well. However, I started with updated conda and set up the channels in the specified order.

I tried removing MetaPhlAn, setting up the channels again, and reinstalling, but I’m still stuck with pyh5ca1d4c\_1. Do you have any advice for resolving this?

---

<div class="post-metadata">

**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\
**Post date:** [May 25, 2020, 11:08am UTC](https://forum.biobakery.org/t/metaphlan3-installation-fails/350/7 "2020-05-25T11:08:34Z")

</div>

Have you tried installing it with `--no-channel-priority` in a clean environment? Cleaning the package cache could help.

---

<div class="post-metadata">

**Author:** ![aimirza](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aimirza/32/499_2.png) [@aimirza](https://forum.biobakery.org/u/aimirza)\
**Post date:** [May 29, 2020, 4:29pm UTC](https://forum.biobakery.org/t/metaphlan3-installation-fails/350/8 "2020-05-29T16:29:58Z")

</div>

> [@fbeghini](#):
>
> metaphlan:3.0–pyh5ca1d4c\_2

**What worked for me is to specify the build when installing** :` conda install metaphlan=3.0=pyh5ca1d4c_2 --no-channel-priority`

---

<div class="post-metadata">

**Author:** ![Tath](https://avatars.discourse-cdn.com/v4/letter/t/65b543/32.png) [@Tath](https://forum.biobakery.org/u/Tath)\
**Post date:** [July 7, 2020, 7:26am UTC](https://forum.biobakery.org/t/metaphlan3-installation-fails/350/9 "2020-07-07T07:26:40Z")

</div>

I’m having the same problem as dkarig.  
I’ve tried everything mentioned in this thread and couldn’t install this build! I tried to install other builds but they failed as well.

---

<div class="post-metadata">

**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\
**Post date:** [July 7, 2020, 12:25pm UTC](https://forum.biobakery.org/t/metaphlan3-installation-fails/350/10 "2020-07-07T12:25:07Z")

</div>

What is your setup? Can you post here the output of `conda info`?

---

<div class="post-metadata">

**Author:** ![Tath](https://avatars.discourse-cdn.com/v4/letter/t/65b543/32.png) [@Tath](https://forum.biobakery.org/u/Tath)\
**Post date:** [July 7, 2020, 1:29pm UTC](https://forum.biobakery.org/t/metaphlan3-installation-fails/350/11 "2020-07-07T13:29:02Z")

</div>

My setup is as follows.

active environment : base  
active env location : /Users/altoids/opt/anaconda3  
shell level : 1  
user config file : /Users/altoids/.condarc  
populated config files : /Users/altoids/.condarc  
conda version : 4.8.3  
conda-build version : 3.18.11  
python version : 3.7.6.final.0  
virtual packages : \_\_osx=10.15.5  
base environment : /Users/altoids/opt/anaconda3 (writable)  
channel URLs : [https://conda.anaconda.org/conda-forge/osx-64](https://conda.anaconda.org/conda-forge/osx-64)  
[https://conda.anaconda.org/conda-forge/noarch](https://conda.anaconda.org/conda-forge/noarch)  
[https://conda.anaconda.org/bioconda/osx-64](https://conda.anaconda.org/bioconda/osx-64)  
[https://conda.anaconda.org/bioconda/noarch](https://conda.anaconda.org/bioconda/noarch)  
[https://repo.anaconda.com/pkgs/main/osx-64](https://repo.anaconda.com/pkgs/main/osx-64)  
[https://repo.anaconda.com/pkgs/main/noarch](https://repo.anaconda.com/pkgs/main/noarch)  
[https://repo.anaconda.com/pkgs/r/osx-64](https://repo.anaconda.com/pkgs/r/osx-64)  
[https://repo.anaconda.com/pkgs/r/noarch](https://repo.anaconda.com/pkgs/r/noarch)  
package cache : /Users/altoids/opt/anaconda3/pkgs  
/Users/altoids/.conda/pkgs  
envs directories : /Users/altoids/opt/anaconda3/envs  
/Users/altoids/.conda/envs  
platform : osx-64  
user-agent : conda/4.8.3 requests/2.22.0 CPython/3.7.6 Darwin/19.5.0 OSX/10.15.5  
UID:GID : 502:20  
netrc file : None  
offline mode : False

---

<div class="post-metadata">

**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\
**Post date:** [July 8, 2020, 7:32am UTC](https://forum.biobakery.org/t/metaphlan3-installation-fails/350/12 "2020-07-08T07:32:52Z")

</div>

Which error it gives you? Are you able to install a specific build?

---

<div class="post-metadata">

**Author:** ![Tath](https://avatars.discourse-cdn.com/v4/letter/t/65b543/32.png) [@Tath](https://forum.biobakery.org/u/Tath)\
**Post date:** [July 8, 2020, 12:50pm UTC](https://forum.biobakery.org/t/metaphlan3-installation-fails/350/13 "2020-07-08T12:50:02Z")

</div>

I could install pyh5ca1d4c\_1.  
The error message is as follows. After this message, many conflicts are listed.

Collecting package metadata (current\_repodata.json): done  
Solving environment: failed with initial frozen solve. Retrying with flexible solve.  
Collecting package metadata (repodata.json): done  
Solving environment: failed with initial frozen solve. Retrying with flexible solve.  
Solving environment: |  
Found conflicts! Looking for incompatible packages.  
This can take several minutes. Press CTRL-C to abort.  
failed | \

UnsatisfiableError: The following specifications were found  
to be incompatible with the existing python installation in your environment:

---

<div class="post-metadata">

**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\
**Post date:** [July 9, 2020, 7:59am UTC](https://forum.biobakery.org/t/metaphlan3-installation-fails/350/14 "2020-07-09T07:59:43Z")

</div>

From the activated environment you have installed metaphlan, can you run `conda list` and post here the results?

---

<div class="post-metadata">

**Author:** ![Tath](https://avatars.discourse-cdn.com/v4/letter/t/65b543/32.png) [@Tath](https://forum.biobakery.org/u/Tath)\
**Post date:** [July 9, 2020, 8:14am UTC](https://forum.biobakery.org/t/metaphlan3-installation-fails/350/15 "2020-07-09T08:14:56Z")

</div>

# Name Version Build Channel

\_ipyw\_jlab\_nb\_ext\_conf 0.1.0 py37\_0  
alabaster 0.7.12 py37\_0  
anaconda 2020.02 py37\_0  
anaconda-client 1.7.2 py37\_0  
anaconda-navigator 1.9.12 py37\_0  
anaconda-project 0.8.4 py\_0  
applaunchservices 0.2.1 py\_0  
appnope 0.1.0 py37\_0  
appscript 1.1.0 py37h1de35cc\_0  
argh 0.26.2 py37\_0  
asn1crypto 1.3.0 py37\_0  
astroid 2.3.3 py37\_0  
astropy 4.0 py37h1de35cc\_0  
atomicwrites 1.3.0 py37\_1  
attrs 19.3.0 py\_0  
autopep8 1.4.4 py\_0  
babel 2.8.0 py\_0  
backcall 0.1.0 py37\_0  
backports 1.0 py\_2  
backports.functools\_lru\_cache 1.6.1 py\_0  
backports.shutil\_get\_terminal\_size 1.0.0 py37\_2  
backports.tempfile 1.0 py\_1  
backports.weakref 1.0.post1 py\_1  
beautifulsoup4 4.8.2 py37\_0  
bitarray 1.2.1 py37h1de35cc\_0  
bkcharts 0.2 py37\_0  
blas 1.0 mkl  
bleach 3.1.0 py37\_0  
blosc 1.16.3 hd9629dc\_0  
bokeh 1.4.0 py37\_0  
boto 2.49.0 py37\_0  
bottleneck 1.3.2 py37h776bbcc\_0  
bzip2 1.0.8 h1de35cc\_0  
ca-certificates 2020.1.1 0  
certifi 2019.11.28 py37\_0  
cffi 1.14.0 py37hb5b8e2f\_0  
chardet 3.0.4 py37\_1003  
click 7.0 py37\_0  
cloudpickle 1.3.0 py\_0  
clyent 1.2.2 py37\_1  
colorama 0.4.3 py\_0  
conda 4.8.2 py37\_0  
conda-build 3.18.11 py37\_0  
conda-env 2.6.0 1  
conda-package-handling 1.6.0 py37h1de35cc\_0  
conda-verify 3.4.2 py\_1  
contextlib2 0.6.0.post1 py\_0  
cryptography 2.8 py37ha12b0ac\_0  
curl 7.68.0 ha441bb4\_0  
cycler 0.10.0 py37\_0  
cython 0.29.15 py37h0a44026\_0  
cytoolz 0.10.1 py37h1de35cc\_0  
dask 2.11.0 py\_0  
dask-core 2.11.0 py\_0  
dbus 1.13.12 h90a0687\_0  
decorator 4.4.1 py\_0  
defusedxml 0.6.0 py\_0  
diff-match-patch 20181111 py\_0  
distributed 2.11.0 py37\_0  
docutils 0.16 py37\_0  
entrypoints 0.3 py37\_0  
et\_xmlfile 1.0.1 py37\_0  
expat 2.2.6 h0a44026\_0  
fastcache 1.1.0 py37h1de35cc\_0  
filelock 3.0.12 py\_0  
flake8 3.7.9 py37\_0  
flask 1.1.1 py\_0  
freetype 2.9.1 hb4e5f40\_0  
fsspec 0.6.2 py\_0  
future 0.18.2 py37\_0  
get\_terminal\_size 1.0.0 h7520d66\_0  
gettext 0.19.8.1 h15daf44\_3  
gevent 1.4.0 py37h1de35cc\_0  
glib 2.63.1 hd977a24\_0  
glob2 0.7 py\_0  
gmp 6.1.2 hb37e062\_1  
gmpy2 2.0.8 py37h6ef4df4\_2  
greenlet 0.4.15 py37h1de35cc\_0  
h5py 2.10.0 py37h3134771\_0  
hdf5 1.10.4 hfa1e0ec\_0  
heapdict 1.0.1 py\_0  
html5lib 1.0.1 py37\_0  
hypothesis 5.5.4 py\_0  
icu 58.2 h4b95b61\_1  
idna 2.8 py37\_0  
imageio 2.6.1 py37\_0  
imagesize 1.2.0 py\_0  
importlib\_metadata 1.5.0 py37\_0  
intel-openmp 2019.4 233  
intervaltree 3.0.2 py\_0  
ipykernel 5.1.4 py37h39e3cac\_0  
ipython 7.12.0 py37h5ca1d4c\_0  
ipython\_genutils 0.2.0 py37\_0  
ipywidgets 7.5.1 py\_0  
isort 4.3.21 py37\_0  
itsdangerous 1.1.0 py37\_0  
jbig 2.1 h4d881f8\_0  
jdcal 1.4.1 py\_0  
jedi 0.14.1 py37\_0  
jinja2 2.11.1 py\_0  
joblib 0.14.1 py\_0  
jpeg 9b he5867d9\_2  
json5 0.9.1 py\_0  
jsonschema 3.2.0 py37\_0  
jupyter 1.0.0 py37\_7  
jupyter\_client 5.3.4 py37\_0  
jupyter\_console 6.1.0 py\_0  
jupyter\_core 4.6.1 py37\_0  
jupyterlab 1.2.6 pyhf63ae98\_0  
jupyterlab\_server 1.0.6 py\_0  
keyring 21.1.0 py37\_0  
kiwisolver 1.1.0 py37h0a44026\_0  
krb5 1.17.1 hddcf347\_0  
lazy-object-proxy 1.4.3 py37h1de35cc\_0  
libarchive 3.3.3 h786848e\_5  
libcurl 7.68.0 h051b688\_0  
libcxx 4.0.1 hcfea43d\_1  
libcxxabi 4.0.1 hcfea43d\_1  
libedit 3.1.20181209 hb402a30\_0  
libffi 3.2.1 h475c297\_4  
libgfortran 3.0.1 h93005f0\_2  
libiconv 1.15 hdd342a3\_7  
liblief 0.9.0 h2a1bed3\_2  
libpng 1.6.37 ha441bb4\_0  
libsodium 1.0.16 h3efe00b\_0  
libspatialindex 1.9.3 h0a44026\_0  
libssh2 1.9.0 ha12b0ac\_1  
libtiff 4.1.0 hcb84e12\_0  
libxml2 2.9.9 hf6e021a\_1  
libxslt 1.1.33 h33a18ac\_0  
llvm-openmp 4.0.1 hcfea43d\_1  
llvmlite 0.31.0 py37h1341992\_0  
locket 0.2.0 py37\_1  
lxml 4.5.0 py37hef8c89e\_0  
lz4-c 1.8.1.2 h1de35cc\_0  
lzo 2.10 h362108e\_2  
markupsafe 1.1.1 py37h1de35cc\_0  
matplotlib 3.1.3 py37\_0  
matplotlib-base 3.1.3 py37h9aa3819\_0  
mccabe 0.6.1 py37\_1  
mistune 0.8.4 py37h1de35cc\_0  
mkl 2019.4 233  
mkl-service 2.3.0 py37hfbe908c\_0  
mkl\_fft 1.0.15 py37h5e564d8\_0  
mkl\_random 1.1.0 py37ha771720\_0  
mock 4.0.1 py\_0  
more-itertools 8.2.0 py\_0  
mpc 1.1.0 h6ef4df4\_1  
mpfr 4.0.1 h3018a27\_3  
mpmath 1.1.0 py37\_0  
msgpack-python 0.6.1 py37h04f5b5a\_1  
multipledispatch 0.6.0 py37\_0  
navigator-updater 0.2.1 py37\_0  
nbconvert 5.6.1 py37\_0  
nbformat 5.0.4 py\_0  
ncurses 6.2 h0a44026\_0  
networkx 2.4 py\_0  
nltk 3.4.5 py37\_0  
nose 1.3.7 py37\_2  
notebook 6.0.3 py37\_0  
numba 0.48.0 py37h6c726b0\_0  
numexpr 2.7.1 py37hce01a72\_0  
numpy 1.18.1 py37h7241aed\_0  
numpy-base 1.18.1 py37h6575580\_1  
numpydoc 0.9.2 py\_0  
olefile 0.46 py37\_0  
openpyxl 3.0.3 py\_0  
openssl 1.1.1d h1de35cc\_4  
packaging 20.1 py\_0  
pandas 1.0.1 py37h6c726b0\_0  
pandoc 2.2.3.2 0  
pandocfilters 1.4.2 py37\_1  
parso 0.5.2 py\_0  
partd 1.1.0 py\_0  
path 13.1.0 py37\_0  
path.py 12.4.0 0  
pathlib2 2.3.5 py37\_0  
pathtools 0.1.2 py\_1  
patsy 0.5.1 py37\_0  
pcre 8.43 h0a44026\_0  
pep8 1.7.1 py37\_0  
pexpect 4.8.0 py37\_0  
pickleshare 0.7.5 py37\_0  
pillow 7.0.0 py37h4655f20\_0  
pip 20.0.2 py37\_1  
pkginfo 1.5.0.1 py37\_0  
pluggy 0.13.1 py37\_0  
ply 3.11 py37\_0  
prometheus\_client 0.7.1 py\_0  
prompt\_toolkit 3.0.3 py\_0  
psutil 5.6.7 py37h1de35cc\_0  
ptyprocess 0.6.0 py37\_0  
py 1.8.1 py\_0  
py-lief 0.9.0 py37h1413db1\_2  
pycodestyle 2.5.0 py37\_0  
pycosat 0.6.3 py37h1de35cc\_0  
pycparser 2.19 py37\_0  
pycrypto 2.6.1 py37h1de35cc\_9  
pycurl 7.43.0.5 py37ha12b0ac\_0  
pydocstyle 4.0.1 py\_0  
pyflakes 2.1.1 py37\_0  
pygments 2.5.2 py\_0  
pylint 2.4.4 py37\_0  
pyodbc 4.0.30 py37h0a44026\_0  
pyopenssl 19.1.0 py37\_0  
pyparsing 2.4.6 py\_0  
pyqt 5.9.2 py37h655552a\_2  
pyrsistent 0.15.7 py37h1de35cc\_0  
pysocks 1.7.1 py37\_0  
pytables 3.6.1 py37h5bccee9\_0  
pytest 5.3.5 py37\_0  
pytest-arraydiff 0.3 py37h39e3cac\_0  
pytest-astropy 0.8.0 py\_0  
pytest-astropy-header 0.1.2 py\_0  
pytest-doctestplus 0.5.0 py\_0  
pytest-openfiles 0.4.0 py\_0  
pytest-remotedata 0.3.2 py37\_0  
python 3.7.6 h359304d\_2  
python-dateutil 2.8.1 py\_0  
python-jsonrpc-server 0.3.4 py\_0  
python-language-server 0.31.7 py37\_0  
python-libarchive-c 2.8 py37\_13  
python.app 2 py37\_10  
pytz 2019.3 py\_0  
pywavelets 1.1.1 py37h1de35cc\_0  
pyyaml 5.3 py37h1de35cc\_0  
pyzmq 18.1.1 py37h0a44026\_0  
qdarkstyle 2.8 py\_0  
qt 5.9.7 h468cd18\_1  
qtawesome 0.6.1 py\_0  
qtconsole 4.6.0 py\_1  
qtpy 1.9.0 py\_0  
readline 7.0 h1de35cc\_5  
requests 2.22.0 py37\_1  
ripgrep 11.0.2 he32d670\_0  
rope 0.16.0 py\_0  
rtree 0.9.3 py37\_0  
ruamel\_yaml 0.15.87 py37h1de35cc\_0  
scikit-image 0.16.2 py37h6c726b0\_0  
scikit-learn 0.22.1 py37h27c97d8\_0  
scipy 1.4.1 py37h9fa6033\_0  
seaborn 0.10.0 py\_0  
send2trash 1.5.0 py37\_0  
setuptools 46.0.0 py37\_0  
simplegeneric 0.8.1 py37\_2  
singledispatch 3.4.0.3 py37\_0  
sip 4.19.8 py37h0a44026\_0  
six 1.14.0 py37\_0  
snappy 1.1.7 he62c110\_3  
snowballstemmer 2.0.0 py\_0  
sortedcollections 1.1.2 py37\_0  
sortedcontainers 2.1.0 py37\_0  
soupsieve 1.9.5 py37\_0  
sphinx 2.4.0 py\_0  
sphinxcontrib 1.0 py37\_1  
sphinxcontrib-applehelp 1.0.1 py\_0  
sphinxcontrib-devhelp 1.0.1 py\_0  
sphinxcontrib-htmlhelp 1.0.2 py\_0  
sphinxcontrib-jsmath 1.0.1 py\_0  
sphinxcontrib-qthelp 1.0.2 py\_0  
sphinxcontrib-serializinghtml 1.1.3 py\_0  
sphinxcontrib-websupport 1.2.0 py\_0  
spyder 4.0.1 py37\_0  
spyder-kernels 1.8.1 py37\_0  
sqlalchemy 1.3.13 py37h1de35cc\_0  
sqlite 3.31.1 ha441bb4\_0  
statsmodels 0.11.0 py37h1de35cc\_0  
sympy 1.5.1 py37\_0  
tbb 2020.0 h04f5b5a\_0  
tblib 1.6.0 py\_0  
terminado 0.8.3 py37\_0  
testpath 0.4.4 py\_0  
tk 8.6.8 ha441bb4\_0  
toolz 0.10.0 py\_0  
tornado 6.0.3 py37h1de35cc\_3  
tqdm 4.42.1 py\_0  
traitlets 4.3.3 py37\_0  
ujson 1.35 py37h1de35cc\_0  
unicodecsv 0.14.1 py37\_0  
unixodbc 2.3.7 h1de35cc\_0  
urllib3 1.25.8 py37\_0  
watchdog 0.10.2 py37h1de35cc\_0  
wcwidth 0.1.8 py\_0  
webencodings 0.5.1 py37\_1  
werkzeug 1.0.0 py\_0  
wheel 0.34.2 py37\_0  
widgetsnbextension 3.5.1 py37\_0  
wrapt 1.11.2 py37h1de35cc\_0  
wurlitzer 2.0.0 py37\_0  
xlrd 1.2.0 py37\_0  
xlsxwriter 1.2.7 py\_0  
xlwings 0.17.1 py37\_0  
xlwt 1.3.0 py37\_0  
xmltodict 0.12.0 py\_0  
xz 5.2.4 h1de35cc\_4  
yaml 0.1.7 hc338f04\_2  
yapf 0.28.0 py\_0  
zeromq 4.3.1 h0a44026\_3  
zict 1.0.0 py\_0  
zipp 2.2.0 py\_0  
zlib 1.2.11 h1de35cc\_3  
zstd 1.3.7 h5bba6e5\_0

---

<div class="post-metadata">

**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\
**Post date:** [July 9, 2020, 9:14am UTC](https://forum.biobakery.org/t/metaphlan3-installation-fails/350/16 "2020-07-09T09:14:18Z")

</div>

It looks like that is not a clean new environment. I’d try to create a new env with just python 3.7 (`conda create -n metaphlan-3.0 python=3.7` and then install metaphlan inside it (`conda activate metaphlan-3.0 && conda install metaphlan=3.0.1`.

Otherwise you should try install it using pip

---

<div class="post-metadata">

**Author:** ![Tath](https://avatars.discourse-cdn.com/v4/letter/t/65b543/32.png) [@Tath](https://forum.biobakery.org/u/Tath)\
**Post date:** [July 10, 2020, 5:07am UTC](https://forum.biobakery.org/t/metaphlan3-installation-fails/350/17 "2020-07-10T05:07:20Z")

</div>

It works!  
Thank you very much for your help.

---

<div class="post-metadata">

**Author:** ![jzski](https://avatars.discourse-cdn.com/v4/letter/j/34f0e0/32.png) [@jzski](https://forum.biobakery.org/u/jzski)\
**Post date:** [July 13, 2020, 8:54pm UTC](https://forum.biobakery.org/t/metaphlan3-installation-fails/350/18 "2020-07-13T20:54:25Z")

</div>

I am having a similar issue with downloading pyh5ca1d4c\_2. I have tried the above steps but after typing condo list I am still seeing that \_1 is installed. Below is conda info. Thanks!

active environment : base  
active env location : /Users/jessica/miniconda3  
shell level : 1  
user config file : /Users/jessica/.condarc  
populated config files : /Users/jessica/.condarc  
conda version : 4.8.3  
conda-build version : 3.19.2  
python version : 3.7.7.final.0  
virtual packages : \_\_osx=10.13.4  
base environment : /Users/jessica/miniconda3 (writable)  
channel URLs : [https://conda.anaconda.org/conda-forge/osx-64](https://conda.anaconda.org/conda-forge/osx-64)  
[https://conda.anaconda.org/conda-forge/noarch](https://conda.anaconda.org/conda-forge/noarch)  
[https://conda.anaconda.org/bioconda/osx-64](https://conda.anaconda.org/bioconda/osx-64)  
[https://conda.anaconda.org/bioconda/noarch](https://conda.anaconda.org/bioconda/noarch)  
[https://repo.anaconda.com/pkgs/main/osx-64](https://repo.anaconda.com/pkgs/main/osx-64)  
[https://repo.anaconda.com/pkgs/main/noarch](https://repo.anaconda.com/pkgs/main/noarch)  
[https://repo.anaconda.com/pkgs/r/osx-64](https://repo.anaconda.com/pkgs/r/osx-64)  
[https://repo.anaconda.com/pkgs/r/noarch](https://repo.anaconda.com/pkgs/r/noarch)  
package cache : /Users/jessica/miniconda3/pkgs  
/Users/jessica/.conda/pkgs  
envs directories : /Users/jessica/miniconda3/envs  
/Users/jessica/.conda/envs  
platform : osx-64  
user-agent : conda/4.8.3 requests/2.23.0 CPython/3.7.7 Darwin/17.5.0 OSX/10.13.4  
UID:GID : 501:20  
netrc file : None  
offline mode : False

---

<div class="post-metadata">

**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\
**Post date:** [July 20, 2020, 8:56am UTC](https://forum.biobakery.org/t/metaphlan3-installation-fails/350/19 "2020-07-20T08:56:14Z")

</div>

Have you tried installing in a new environment?

---

<div class="post-metadata">

**Author:** ![rkamales](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/rkamales/32/332_2.png) [@rkamales](https://forum.biobakery.org/u/rkamales)\
**Post date:** [July 27, 2020, 3:25am UTC](https://forum.biobakery.org/t/metaphlan3-installation-fails/350/20 "2020-07-27T03:25:37Z")

</div>

I am getting the same error when I run Humann3 as follows:

humann3 --protein-database /media/sf\_data/uniref/uniref --threads 4 -i $f -o output --output-format biom --remove-stratified-output --output-max-decimals 0

Output files will be written to: /media/sf\_data/output  
Decompressing gzipped file …

Removing spaces from identifiers in input file …

WARNING: Can not call software version for bowtie2

Running metaphlan …

CRITICAL ERROR: Error executing: /home/rkamales/anaconda3/envs/biobakery3/bin/metaphlan /media/sf\_data/output/CCO12148-0070-1-1-C0WT2\_S6\_L001\_R1\_001\_humann\_temp/tmpwhm\_fon8/tmp2f9om6xb -t rel\_ab -o /media/sf\_data/output/CCO12148-0070-1-1-C0WT2\_S6\_L001\_R1\_001\_humann\_temp/CCO12148-0070-1-1-C0WT2\_S6\_L001\_R1\_001\_metaphlan\_bugs\_list.tsv --input\_type fastq --bowtie2out /media/sf\_data/output/CCO12148-0070-1-1-C0WT2\_S6\_L001\_R1\_001\_humann\_temp/CCO12148-0070-1-1-C0WT2\_S6\_L001\_R1\_001\_metaphlan\_bowtie2.txt --nproc 4

Error message returned from metaphlan :

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

File /home/rkamales/anaconda3/envs/biobakery3/lib/python3.7/site-packages/metaphlan/metaphlan\_databases/file\_list.txt already present!  
Traceback (most recent call last):  
File “/home/rkamales/anaconda3/envs/biobakery3/bin/metaphlan”, line 10, in   
sys.exit(main())  
File “/home/rkamales/anaconda3/envs/biobakery3/lib/python3.7/site-packages/metaphlan/metaphlan.py”, line 1187, in main  
pars[‘index’] = check\_and\_install\_database(pars[‘index’], pars[‘bowtie2db’], pars[‘bowtie2\_build’], pars[‘nproc’], pars[‘force\_download’])  
File “/home/rkamales/anaconda3/envs/biobakery3/lib/python3.7/site-packages/metaphlan/metaphlan.py”, line 610, in check\_and\_install\_database  
download\_unpack\_tar(FILE\_LIST, index, bowtie2\_db, bowtie2\_build, nproc)  
File “/home/rkamales/anaconda3/envs/biobakery3/lib/python3.7/site-packages/metaphlan/metaphlan.py”, line 463, in download\_unpack\_tar  
url\_tar\_file = ls\_f[“mpa\_” + download\_file\_name + “.tar”]  
KeyError: ‘mpa\_mpa\_v30\_CHOCOPhlAn\_201901.tar’

My Conda Info is:

active environment : biobakery3  
active env location : /home/rkamales/anaconda3/envs/biobakery3  
shell level : 2  
user config file : /home/rkamales/.condarc  
populated config files : /home/rkamales/.condarc  
conda version : 4.8.3  
conda-build version : 3.18.11  
python version : 3.8.3.final.0  
virtual packages : \_\_glibc=2.27  
base environment : /home/rkamales/anaconda3 (writable)  
channel URLs : [https://conda.anaconda.org/biobakery/linux-64](https://conda.anaconda.org/biobakery/linux-64)  
[https://conda.anaconda.org/biobakery/noarch](https://conda.anaconda.org/biobakery/noarch)  
[https://conda.anaconda.org/conda-forge/linux-64](https://conda.anaconda.org/conda-forge/linux-64)  
[https://conda.anaconda.org/conda-forge/noarch](https://conda.anaconda.org/conda-forge/noarch)  
[https://conda.anaconda.org/bioconda/linux-64](https://conda.anaconda.org/bioconda/linux-64)  
[https://conda.anaconda.org/bioconda/noarch](https://conda.anaconda.org/bioconda/noarch)  
[https://repo.anaconda.com/pkgs/main/linux-64](https://repo.anaconda.com/pkgs/main/linux-64)  
[https://repo.anaconda.com/pkgs/main/noarch](https://repo.anaconda.com/pkgs/main/noarch)  
[https://repo.anaconda.com/pkgs/r/linux-64](https://repo.anaconda.com/pkgs/r/linux-64)  
[https://repo.anaconda.com/pkgs/r/noarch](https://repo.anaconda.com/pkgs/r/noarch)  
package cache : /home/rkamales/anaconda3/pkgs  
/home/rkamales/.conda/pkgs  
envs directories : /home/rkamales/anaconda3/envs  
/home/rkamales/.conda/envs  
platform : linux-64  
user-agent : conda/4.8.3 requests/2.24.0 CPython/3.8.3 Linux/5.3.0-28-generic ubuntu/18.04.4 glibc/2.27  
UID:GID : 1000:1000  
netrc file : None  
offline mode : False

[Next page](https://forum.biobakery.org/t/metaphlan3-installation-fails/350.md?page=2)