Failed to get rootless runtime dir

[tbazilegith]

Hi,
Describe the bug
Installed pgap 2023-05-17.build6771, below is my directory
input-2023-05-17.build6771 pgap_2023-05-17.build6771.sif pgap.py test_genomes test_genomes-2023-05-17.build6771 VERSION
To Reproduce
I ran the test,
./pgap.py -r -o results test_genomes/MG37/input.yaml

I had this issues
WARN[0000] Failed to get rootless runtime dir for DefaultAPIAddress: lstat /run/user/6210: no such file or directory
Error: creating events dirs: mkdir /run/user/6210: permission denied
Traceback (most recent call last):
File "/user/repos/ncbi/pgap/./pgap.py", line 1018, in main
retcode = p.launch()
File "/user/repos/ncbi/pgap/./pgap.py", line 488, in launch
self.record_runtime(f)
File "/user/repos/ncbi/pgap/./pgap.py", line 417, in record_runtime
result = subprocess.run(cmd, stdin=subprocess.DEVNULL, check=True, stdout=subprocess.PIPE)
File "/apps/conda/4.12.0/lib/python3.10/subprocess.py", line 524, in run

Expected behavior
A clear and concise description of what you expected to happen.

Software versions (please complete the following information):

• OS: [e.g. CentOS 7, Windows 10, etc.]
• pgap.py --version, or docker image version.
• Docker (or other container runner) version. [e.g. docker --version]

Log Files

Docker command: /usr/bin/podman run -i --rm --volume /user/repos/ncbi/pgap/input-2023-05-17.build6771:/pgap/input:ro,Z --volume /user/repos/ncbi/pgap/test_genomes/MG37:/pgap/user_input:Z --volume /blue/bphl-/user/repos/ncbi/pgap/test_genomes/MG37/pgap_input_5ksvccmq.yaml:/pgap/user_input/pgap_input.yaml:ro,Z --volume /scratch/local/8947500:/tmp:rw --volume /user/repos/ncbi/pgap/results:/pgap/output:rw,Z docker.io/ncbi/pgap:2023-05-17.build6771 cwltool --timestamps --debug --disable-color --preserve-entire-environment --outdir /pgap/output pgap/pgap.cwl /pgap/user_input/pgap_input.yaml
Additional context

Thanks!
TJ

[azat-badretdin]

Thank you for your report, TJ!

The issue seems to be related to specifics of your podman installation. It is a bit puzzling that a read-only command that executes cat under a podman call produces what seems to be a write operation (mkdir).

We will have a look and discuss what we can do here.

[azat-badretdin]

It is unlikely that we can do anything here on our side, the mentioned directory does not resemble anything that we used.

I would suggest to reinstall Podman or reset it in some other way to see if that helps.