Metaphlan3 installation fails

Andrei_Prodan · April 18, 2020, 4:56am

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

fbeghini · April 18, 2020, 6:00pm

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.

Andrei_Prodan · April 19, 2020, 11:11am

the metaphalan3 version installed by conda is:

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

fbeghini · April 20, 2020, 9:57am

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

Andrei_Prodan · April 20, 2020, 10:18am

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!

dkarig · May 24, 2020, 3:26pm

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?

fbeghini · May 25, 2020, 11:08am

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

aimirza · May 29, 2020, 4:29pm

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

Tath · July 7, 2020, 7:26am

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.

fbeghini · July 7, 2020, 12:25pm

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

Tath · July 7, 2020, 1:29pm

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

fbeghini · July 8, 2020, 7:32am

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

Tath · July 8, 2020, 12:50pm

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:

fbeghini · July 9, 2020, 7:59am

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

Tath · July 9, 2020, 8:14am

fbeghini · July 9, 2020, 9:14am

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

Tath · July 10, 2020, 5:07am

It works!
Thank you very much for your help.

jzski · July 13, 2020, 8:54pm

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

fbeghini · July 20, 2020, 8:56am

Have you tried installing in a new environment?

rkamales · July 27, 2020, 3:25am

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

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Metaphlan3 installation fails

Name Version Build Channel

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