Cannot open file '/tmp

[wenkui123]

Hello, I want to use AMRFinderPlus in docker container , , but I get the following error:

root@38d842152c2e:/amrfinder# ./amrfinder -u Running: ./amrfinder -u Software directory: '/amrfinder/' Software version: 3.11.2

ERROR Reading file '/tmp/amrfinder.yz1fUh/log' Cannot open file '/tmp/amrfinder.yz1fUh/log'

HOSTNAME: 38d842152c2e SHELL: ? PWD: /amrfinder PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/amrfinder Progam name: amrfinder Command line: ./amrfinder -u

Why does this error occu ? How can I solve this problem? thanks

[evolarjun]

Hi @wenkui123 ,

I haven't been able to reproduce your issue, perhaps there is an additional restriction on /tmp or growing the container in your docker environment? I will continue to investigate.

However you shouldn't need to run amrfinder -u if you're using the latest image (right now tag 3.11.2-2022-12-19.1) because we update the container with the latest software and database on every release. If you want to use it in non-interactive mode here's an example of how we suggest using it:

# Example run on a local file with 8 threads
docker run --rm -v ${PWD}:/data ncbi/amr amrfinder -p test_prot.fa --threads 8

I just realized we don't have any documentation about how to use the docker container in our documentation. We'll work on that.

Let us know if you can run AMRFinderPlus on an external sequence. I will continue trying to figure out what's going wrong in your case.

[vbrover]

Do you have a permission on /tmp/amrfinder.yz1fUh/log? Is there a free space for /tmp/amrfinder.yz1fUh/log?

Could you run this

./amrfinder -u --debug --log aa

and post the contents of the file aa?