Job Error - Annotation File Field or Mounting Path Issue?

[birdbysnow]

Hi there, I expect this is actually a system configuration issue, but I thought I'd check in case it is a bug or you have some suggestion on how I can resolve the problem.

System Info
I'm using Ubuntu in Windows Subsystem for Linux (WSL) to try and run the example from your documentation. Since I actually have Docker Desktop for Windows installed, I decided to use BASH to call Docker CLI and connect to it as a remote daemon. The configuration details are described here - the only difference is that I installed docker.io instead of ce in WSL because I saw it was used in your demo and other users indicated that the change was not problematic for them.

As far as I can tell, everything connects properly - I get reponses from the dameon, e.g. info, images, and containers (e.g. docker_images.txt). Also, as far as I can tell from creating a container, volume mounts work as expected. I checked and my user is in the docker group. Unfortunately, cwl-runner still fails, so I am unable to get run either the pipeline script or cwl-runner directly (i.e. using the json and cwl files generated by the former).

Below are the commands, along with the results.

Via Script -
lisa@BirdBySnow-SG:/c/Users/lisae/git/GALES/bin$ ./run_prok_pipeline -i ../test_data/genomes/E_coli_k12_dh10b.fna -od /tmp/demo -v cheetah -rd /dbs > console_log.txt 2>&1
console_log.txt
script_output.zip

Via Direct -
cwl-runner /tmp/demo/prok-annotation-cheetah.cwl /tmp/demo/prok-annotation-cheetah.json > cwl_runner_console_log.txt 2>&1
cwl_runner_console_log.txt

Suggestions/help?
Thanks, Lisa

[jorvis]

Hmm, it's definitely the Prodigal step there which isn't returning successfully. I tried to create a docker string which would just run that step based on the input paths you specified. Give it a try (but edit if you see anything there which doesn't match your setup.)

docker run -i --volume=/tmp:/output --volume=/c/Users/lisae/git/GALES/test_data/genomes/E_coli_k12_dh10b.fna:/var/lib/cwl/stg31661eb0-f913-4e6f-8b38-0c4fbc506fed/E_coli_k12_dh10b.fna:ro --env=TMPDIR=/tmp jorvis/gales-gce prodigal -i /var/lib/cwl/stg31661eb0-f913-4e6f-8b38-0c4fbc506fed/E_coli_k12_dh10b.fna -f gff -o /ouput/prodigal.annotation.gff -a /output/prodigal.annotation.faa

What do you get from that?

[birdbysnow]

Thanks for the quick response! The info matches my system (assuming the general /local/path:/image/path format still applies), so I haven't changed anything. Unfortunately, the response isn't super verbose -

lisa@BirdBySnow-SG:/c/Users/lisae/git/GALES/bin$ docker run -i --volume=/tmp:/output --volume=/c/Users/lisae/git/GALES/test_data/genomes/E_coli_k12_dh10b.fna:/var/lib/cwl/stg31661eb0-f913-4e6f-8b38-0c4fbc506fed/E_coli_k12_dh10b.fna:ro --env=TMPDIR=/tmp jorvis/gales-gce prodigal -i /var/lib/cwl/stg31661eb0-f913-4e6f-8b38-0c4fbc506fed/E_coli_k12_dh10b.fna -f gff -o /ouput/prodigal.annotation.gff -a /output/prodigal.annotation.faa
-------------------------------------
PRODIGAL v2.6.3 [February, 2016]
Univ of Tenn / Oak Ridge National Lab
Doug Hyatt, Loren Hauser, et al.
-------------------------------------

Error: can't open output file /ouput/prodigal.annotation.gff.

Also, in case it helps, it doesn't look like prodigal.annotation.gff was created anywhere else either.

[jorvis]

Looks like a typo there. 'ouput' instead of 'output' in the path.