$ metaphlan --version
MetaPhlAn version 3.0.7 (09 Dec 2020)
$ humann --version
humann v3.0.0.alpha.4
$ biobakery_workflows --version
biobakery_workflows v3.0.0-alpha.7
When attempting to run:
biobakery_workflows_databases --install wmgx
according to: Installing the workflows with pip · biobakery/biobakery_workflows Wiki · GitHub
I get:
Could not locate a Bowtie index corresponding to basename "/u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901"
looking in /u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/metaphlan/metaphlan_databases/ I see the following:
$ ls /u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/metaphlan/metaphlan_databases/mpa_v31_CHOCOPhlAn_201901.
mpa_v31_CHOCOPhlAn_201901.1.bt2 mpa_v31_CHOCOPhlAn_201901.3.bt2 mpa_v31_CHOCOPhlAn_201901.fna.bz2 mpa_v31_CHOCOPhlAn_201901.pkl mpa_v31_CHOCOPhlAn_201901.rev.2.bt2
mpa_v31_CHOCOPhlAn_201901.2.bt2 mpa_v31_CHOCOPhlAn_201901.4.bt2 mpa_v31_CHOCOPhlAn_201901.md5 mpa_v31_CHOCOPhlAn_201901.rev.1.bt2 mpa_v31_CHOCOPhlAn_201901.tar
indeed the step:
metaphlan --install --nproc 2
does not download the version 30 of the DB but only the 31 as you can see from:
$ metaphlan --install --nproc 2
Downloading http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/mpa_latest
Downloading file of size: 0.00 MB
0.01 MB 31507.69 % 55.54 MB/sec 0 min -0 sec
Downloading MetaPhlAn database
Please note due to the size this might take a few minutes
Downloading http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/mpa_v31_CHOCOPhlAn_201901.tar
Downloading file of size: 407.85 MB
Building a SMALL index85 MB/sec 0 min 0 sec
407.85 MB 100.00 % 2.85 MB/sec 0 min 0 sec
Downloading http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/mpa_v31_CHOCOPhlAn_201901.md5
Downloading file of size: 0.00 MB
0.01 MB 12800.00 % 186.18 MB/sec 0 min -0 sec
Decompressing /u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/metaphlan/metaphlan_databases/mpa_v31_CHOCOPhlAn_201901.fna.bz2 into /u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/metaphlan/metaphlan_databases/mpa_v31_CHOCOPhlAn_201901.fna
Building Bowtie2 indexes
Removing uncompress database /u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/metaphlan/metaphlan_databases/mpa_v31_CHOCOPhlAn_201901.fna
Download complete
The database is installed
Is it possible that the metaphian DB has been updated from version 30 to 31 and that biobakery needs to be updated? Or should I do a manual download from Index of /biobakery3/metaphlan_databases?
Thanks,
RD