Hello,
I am currently trying to use Metaphlan2 on a remote supercomputer. When downloading the database, it naturally wants to download to the local install on the supercomputer. However, the admins advised that the database be downloaded in my home directory. How would I go about doing this? I tried to manually download the db and specify the directory with -bowtie2db, but I still get the same error.
Thanks!
Hi,
you can download the database in your home directory by running
metaphlan2.py --install --bowtie2db $HOME/mpa_v20_m20
and then running MetaPhlAn2 with the --bowtie2db $HOME/mpa_v20_m20 parameter
Which error is giving you when running with `–bowtie2db?
Hello!
I recreated your command (in my home directory) to install the database
HOME=/home/aubhah/
/opt/asn/apps/anaconda_2-5.2.0/bin/metaphlan2.py --install --bowtie2db
$HOME/mpa_v20_m20
and received this error:
Downloading MetaPhlAn2 database
Please note due to the size this might take a few minutes
ERROR: The directory is not writeable: /opt/asn/apps/anaconda_2-
5.2.0/bin/databases. Please modify the permissions.You don’t need to declare a new HOME variable since is set by default by the system.
Is $HOME/mpa_v20_m20 on the same line of metaphlan2.py --install --bowtie2db ?
Which version of MetaPhlAn2 are you using?
I took away the
home=/home/aubhah/
and received the same error.
Downloading MetaPhlAn2 database
Please note due to the size this might take a few minutes
ERROR: The directory is not writeable: /opt/asn/apps/anaconda_2-5.2.0/bin/databases. Please modify the permissions.
It is on the same line, that was a copying error! I am currently using v2.7.5
Okay, I can replicate the same error by using MetaPhlAn2 2.7.5. It seems that was a bug resolved in the next versions, you can download the latest version of MetaPhlAn2 (v2.7.8) from here.
Awesome, thanks for your help! I will have the admins update the version.
Hello,
We updated the version and I got it to work. Thanks so much for your help!