The bioBakery help forum

Metaphlan 3 md5 error

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.