I am trying to run HUMAnN with a fresh install using conda, my installed versions are humann v3.7 and metaphlan v4.0.6. This is my 3rd or fourth attempt at solving this issue. I have tried removing the files and redownloading the database multiple times as suggested here (MetaPhlan Database) - note the recent post at the bottom with the same issue as I am having.
I also tried to use vJan21 but when I started running humann it automatically tried to install vOct22 anyways and failed with the same error. I also tried using the --metaphlan-options “-bowtie2db /path/to/database” addition to the command as well pointing to an installation of vJan21 which also did not work.
(HUMANN) [clairmontl@biocomp-0-1 humann]$ metaphlan --install
Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_latest
Downloading file of size: 0.00 MB
0.01 MB 25600.00 % 52.43 MB/sec 0 min -0 sec
Downloading MetaPhlAn database
Please note due to the size this might take a few minutes
\Downloading and uncompressing indexes
Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/mpa_vOct22_CHOCOPhlAnSGB_202212_bt2.tar
Downloading file of size: 20348.27 MB
20348.27 MB 100.00 % 24.63 MB/sec 0 min -0 sec
Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/mpa_vOct22_CHOCOPhlAnSGB_202212_bt2.md5
Downloading file of size: 0.00 MB
Warning: Unable to extract /home/AAFC-AAC/clairmontl/miniconda3/envs/HUMANN/lib/python3.10/site-packages/metaphlan/metaphlan_databases/mpa_vOct22_CHOCOPhlAnSGB_202212_bt2.tar.
Downloading and uncompressing additional files
Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vOct22_CHOCOPhlAnSGB_202212.tar
Warning: Unable to download http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vOct22_CHOCOPhlAnSGB_202212.tar
Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vOct22_CHOCOPhlAnSGB_202212.md5
Warning: Unable to download http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vOct22_CHOCOPhlAnSGB_202212.md5
File “/home/AAFC-AAC/clairmontl/miniconda3/envs/HUMANN/lib/python3.10/site-packages/metaphlan/metaphlan_databases/mpa_vOct22_CHOCOPhlAnSGB_202212.md5” not found!
File “/home/AAFC-AAC/clairmontl/miniconda3/envs/HUMANN/lib/python3.10/site-packages/metaphlan/metaphlan_databases/mpa_vOct22_CHOCOPhlAnSGB_202212.tar” not found!
MD5 checksums not found, something went wrong!