I’ve tried running metaphlan 3 on our data multiple times, but I keep getting repeated errors like this one. Clearing the metaphlan database directory as instructed doesn’t fix the problem.
Downloading MetaPhlAn database
Please note due to the size this might take a few minutes
File /opt/anaconda/lib/python3.7/site-packages/metaphlan/metaphlan_databases/file_list.txt already present!
File /opt/anaconda/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.tar already present!
File /opt/anaconda/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.md5 already present!
MD5 checksums do not correspond! If this happens again, you should remove the database files and rerun MetaPhlAn so they are re-downloaded
Have you removed also the tar and the md5 file? I have run metaphlan --install from a clean install and the checksum is OK
Hi, I am having the same issue with metaphlan2 (v2.7.7). When I try to download the bowtie2db with the following onto my personal server space (operating on HPC) I get an error.
[jfessler@cri16cn057 metaphlan2]$ metaphlan2.py --install --bowtie2db mpa_v20_m200
Downloading MetaPhlAn2 database
Please note due to the size this might take a few minutes
Downloading https://bitbucket.org/biobakery/metaphlan2/downloads/mpa_v20_m200.tar
Enter username for Bitbucket.org HTTP at bitbucket.org:jfessler22
Enter password for in Bitbucket.org HTTP at bitbucket.org:
Downloading https://bitbucket.org/biobakery/metaphlan2/downloads/mpa_v20_m200.md5
Enter username for Bitbucket.org HTTP at bitbucket.org:jfessler22
Enter password for in Bitbucket.org HTTP at bitbucket.org:
MD5 checksums not found, something went wrong!
Similarly if I try to run metaphlan2 pointing towards a new folder to download the bowtie2db I get the same error.
The result is a folder created with two empty files: mpa_v20_m200.md5 and mpa_v20_m200.tar
Any suggestions? The MetaPhlAn software has been installed onto our HPC by system admin.
Oh I see now in this other thread that this version might be pointing to the incorrect location for the download. I will see if our system admin can update our version.
I reinstalled metaphlan3 and now I get the following error when I run metaphlan --install:
Downloading MetaPhlAn database
Please note due to the size this might take a few minutes
File /opt/anaconda/envs/mpa/lib/python3.6/site-packages/metaphlan/metaphlan_databases/file_list.txt already present!
Traceback (most recent call last):
File “/opt/anaconda/envs/mpa/bin/metaphlan”, line 10, in
sys.exit(main())
File “/opt/anaconda/envs/mpa/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 “/opt/anaconda/envs/mpa/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 “/opt/anaconda/envs/mpa/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_v30_CHOCOPhlAn_201901.tar’
What’s the problem?
It seems you have installed an older build of MetaPhlAn 3, probably pyh5ca1d4c_2. This error has been corrected in newer builds (latest one is pyh5ca1d4c_4 https://anaconda.org/bioconda/metaphlan/3.0/download/noarch/metaphlan-3.0-pyh5ca1d4c_4.tar.bz2)
Thanks, I installed the linked file using conda install, and metaphlan --install is now working. Someone should update the package in the conda online repository.
The tarball is linked to the Bioconda MetaPhlAn package, did you had issues installing MetaPhlAn using conda install metaphlan, such as not fetching the latest build?
I already had metaphlan 3 installed but when I ran conda update metaphlan it said there were no updates to the package.