Cannot download any databases using amrfinder -u

[padpadpadpad]

Hi all

Successfully downloaded ncbi-amrfinderplus into its own conda environment, but when I run amrfinder -u I receive the error:

`*** ERROR ***

Cannot create directory "/home2"`

Complete output is attached.

Any thoughts let me know. I think it could be to do with permissions given I do not have admin rights, but I can easily download things onto my area of the server.

Cheers
Dan

[vbrover]

Could you create the directory /home2/ISAD/dp415/miniconda3/envs/amr_env/share/amrfinderplus/data manually and then run amrfinder -u?

Also, what exit code does this command return: ls /home2?

[padpadpadpad]

I have created the directory manually but the error remains after re-running the command

ls /home2 gives the error ls: cannot open directory '/home2': Permission denied.

I do not have access until /home2/ISAD/dp415.

[vbrover]

Could you post your screen output after amrfinder -u?

[padpadpadpad]

It remains the same as in my first post (hopefully there is a screenshot on the original post).

[vbrover]

The first post said that the directory

/home2/ISAD/dp415/miniconda3/envs/amr_env/share/amrfinderplus/data

could not be created.
Now that you have created this directory manually, there should be another error about failing to create the directory

/home2/ISAD/dp415/miniconda3/envs/amr_env/share/amrfinderplus/data/2021-06-01.1

amrfinder_update of this version will fail because your /home2 is not readable (this is our bug which we will fix in a future amrfinder version).
My idea to circumvent this bug is to create the needed directories manually.

[padpadpadpad]

Thanks

I tried to make the next directory /home2/ISAD/dp415/miniconda3/envs/amr_env/share/amrfinderplus/data/2021-06-01.1.

I then attempted amrfinder -u and did receive a new error (screenshot attached). Is there anyway to manually download the database and tell amrfinder to use that?

[vbrover]

Please try:

amrfinder -U

(Capital "U")

[padpadpadpad]

This works. Should I have been doing that all the time.

Thank you very much.

[vbrover]

amrfinder -U does not check the existing version and forces updating the data files.

You have downloaded the most recent data files.
The next version data files will most likely come with the updated software where this bug will be fixed.
So that you will be able to use the regular amrfinder -u without hacks.

[evolarjun]

We just made a release version 3.10.11 that should address this issue. It may take a while to percolate through bioconda.