You can find the user manual on the GitHub repository here (https://github.com/biobakery/humann) and an extensive tutorial on the bioBakery wiki here (https://github.com/biobakery/biobakery/wiki/humann3)
It seems i meet the same question as in this question. i have operated as you suggest but when i run conda list | grep metaphlan
(metaphlan-3.0) wangzhenyu@wangzhenyudeMacBook-Pro metaphlan_database % conda list | grep metaphlan
packages in environment at /Users/wangzhenyu/opt/miniconda3/envs/metaphlan-3.0:
metaphlan 3.0 pyh5ca1d4c_1 bioconda
It seems like metaphlan is not updated, how could i solve this problem?
thank you!
Can you post the list of the installed packages in the metaphlan-3.0 environment? Have you configured correctly the conda channels?
Just jumping onto this topic; I’m having similar problems running the metaphlan3 in a newly made python environment. I ran metaphlan --install and got the same md5 error as above.
Should I repost this as a different topic?
Below are the installed packages:
bcbio-gff 0.6.6
biom-format 2.1.8
biopython 1.77
certifi 2020.6.20
chardet 3.0.4
click 7.1.2
CMSeq 1.0.1
cycler 0.10.0
Cython 0.29.21
DendroPy 4.4.0
future 0.17.1
h5py 2.10.0
idna 2.10
kiwisolver 1.2.0
matplotlib 3.2.1
MetaPhlAn 3.0.1
numpy 1.19.1
pandas 1.0.5
PhyloPhlAn 3.0.0
pip 20.2.1
pyparsing 2.4.7
pysam 0.15.4
python-dateutil 2.8.1
pytz 2020.1
requests 2.24.0
scipy 1.4.1
seaborn 0.10.1
setuptools 49.3.1
six 1.15.0
urllib3 1.25.10
wheel 0.34.2
Thanks so much for any feed back.
The setup seems OK. Have you tried to manually remove the tar and md5 files and run again the installation?
Thanks for the feedback! Did just that and it progressed further, but resulted in a different error. Output pasted below:
(MetaphlanHumann_env) [krey@cedar5 metaphlan_databases]$ metaphlan --install
Downloading MetaPhlAn database
Please note due to the size this might take a few minutes
File /home/krey/MetaphlanHumann_env/lib/python3.8/site-packages/metaphlan/metaphlan_databases/file_list.txt already present!
Downloading https://www.dropbox.com/sh/7qze7m7g9fe2xjg/AADlxibskzbPHPoDl6S-FyKka/mpa_v30_CHOCOPhlAn_201901.tar?dl=1
Downloading file of size: 366.62 MB
366.62 MB 100.00 % 1.80 MB/sec 0 min -0 sec
Downloading https://www.dropbox.com/sh/7qze7m7g9fe2xjg/AACTzoUYDqZps8u2JqWCNCODa/mpa_v30_CHOCOPhlAn_201901.md5?dl=1
Downloading file of size: 0.00 MB
0.01 MB 12800.00 % 5.84 MB/sec 0 min -0 sec
Decompressing /home/krey/MetaphlanHumann_env/lib/python3.8/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.fna.bz2 into /home/krey/MetaphlanHumann_env/lib/python3.8/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.fna
Traceback (most recent call last):
File “/home/krey/MetaphlanHumann_env/bin/metaphlan”, line 8, in
sys.exit(main())
File “/home/krey/MetaphlanHumann_env/lib/python3.8/site-packages/metaphlan/metaphlan.py”, line 916, in main
pars[‘index’] = check_and_install_database(pars[‘index’], pars[‘bowtie2db’], pars[‘bowtie2_build’], pars[‘nproc’], pars[‘force_download’])
File “/home/krey/MetaphlanHumann_env/lib/python3.8/site-packages/metaphlan/init.py”, line 290, in check_and_install_database
download_unpack_tar(FILE_LIST, index, bowtie2_db, bowtie2_build, nproc)
File “/home/krey/MetaphlanHumann_env/lib/python3.8/site-packages/metaphlan/init.py”, line 181, in download_unpack_tar
bt2_build_output = subp.check_output([bowtie2_build, ‘–usage’], stderr=subp.STDOUT)
File “/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.8.2/lib/python3.8/subprocess.py”, line 411, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File “/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.8.2/lib/python3.8/subprocess.py”, line 489, in run
with Popen(*popenargs, **kwargs) as process:
File “/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.8.2/lib/python3.8/subprocess.py”, line 854, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File “/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.8.2/lib/python3.8/subprocess.py”, line 1702, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: ‘bowtie2-build’
Sorry for the delayed reply; removing the files and running the installation again fixed the issue. On my setup for this software, I had to update my version of glpk to get everything to work but once I did so Humann3 ran without issue.