The bioBakery help forum

Metaphlan3 installation fails

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’) also fails to install with:

Error response from daemon: manifest for quay.io/biocontainers/metaphlan:latest not found: manifest unknown: manifest unknown

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.

the metaphalan3 version installed by conda is:

“bioconda/noarch::metaphlan-3.0-pyh5ca1d4c_1”

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, 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

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!

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?

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

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

1 Like

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.

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

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/noarch
https://conda.anaconda.org/bioconda/osx-64
https://conda.anaconda.org/bioconda/noarch
https://repo.anaconda.com/pkgs/main/osx-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/osx-64
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

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

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:

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

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

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

It works!
Thank you very much for your help.

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/noarch
https://conda.anaconda.org/bioconda/osx-64
https://conda.anaconda.org/bioconda/noarch
https://repo.anaconda.com/pkgs/main/osx-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/osx-64
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

Have you tried installing in a new environment?

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/noarch
https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://conda.anaconda.org/bioconda/linux-64
https://conda.anaconda.org/bioconda/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
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