No such file or directory: '/inputs/idh1_config.yaml'

[taherimo]

I followed the steps to run the pipeline using docker, but the config file cannot be found by the pipeline:

Traceback (most recent call last):
  File "run_snakemake.py", line 375, in <module>
    main()
  File "run_snakemake.py", line 333, in main
    with open(args.configfile) as configfile:
FileNotFoundError: [Errno 2] No such file or directory: '/inputs/idh1_config.yaml'

Even when I pass the absolute path of the yaml file to the --configfile= argument I get same error.

[timodonnell]

Are you mounting a volume (docker -v argument) for the input directory?

…

On Sun, Jan 12, 2025 at 9:46 AM taherimo ***@***.***> wrote: I followed the steps to run the pipeline using docker, but the config file cannot be found by the pipeline: Traceback (most recent call last): File "run_snakemake.py", line 375, in <module> main() File "run_snakemake.py", line 333, in main with open(args.configfile) as configfile: FileNotFoundError: [Errno 2] No such file or directory: '/inputs/idh1_config.yaml' Even when I pass the absolute path of the yaml file to the --configfile= argument I get same error. — Reply to this email directly, view it on GitHub <#164>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AADSHOHEAUWHO55NSO6A4WD2KJ54RAVCNFSM6AAAAABVBDAVTOVHI2DSMVQWIX3LMV43ASLTON2WKOZSG44DENJSGIZTENA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[taherimo]

@timodonnell I created input, output, and reference-genome directories as described in the README file and copied the required files (fastq, vcf, bed, etc.) into the input and reference-genome directories.

Also, docker -v returns my docker version (Docker version 27.4.1, build b9d17ea).

[julia326]

Could you paste the full docker command you're using to run the pipeline? Also worth checking, do you see the idh1_config.yaml file in whatever directory you're mounting as /inputs? (docker -v <realpath>:<mountpath> is how the -v flag works)

[taherimo]

@julia326 Yes I have three subdirectories under a directory I created for this purpose (neoantigen_vaccine_pipeline_docker_volumes):

inputs outputs reference-genome

I created them as described in the manual. Also, the idh1_config.yaml file exists in the input directory.

Here is my full docker command:

docker run -it -v /home/taherimo/neoantigen_vaccine_pipeline_docker_volumes/inputs -v /home/taherimo/neoantigen_vaccine_pipeline_docker_volumes/outputs -v /home/taherimo/neoantigen_vaccine_pipeline_docker_volumes/reference-genome openvax/neoantigen-vaccine-pipeline:latest --configfile=/inputs/idh1_config.yaml

[julia326]

@taherimo I think the issue is that your docker command is missing colons in specifying the mounts. Try running:

docker run -it -v /home/taherimo/neoantigen_vaccine_pipeline_docker_volumes:/inputs -v /home/taherimo/neoantigen_vaccine_pipeline_docker_volumes:/outputs -v /home/taherimo/neoantigen_vaccine_pipeline_docker_volumes:/reference-genome openvax/neoantigen-vaccine-pipeline:latest --configfile=/inputs/idh1_config.yaml

[taherimo]

@julia326 I ran exactly the command you mentioned (included colons). But I still get same error:

Traceback (most recent call last):
  File "run_snakemake.py", line 375, in <module>
    main()
  File "run_snakemake.py", line 333, in main
    with open(args.configfile) as configfile:
FileNotFoundError: [Errno 2] No such file or directory: '/inputs/idh1_config.yaml'

[julia326]

@taherimo I just realized I missed the part above where you have subfolders within /home/taherimo/neoantigen_vaccine_pipeline_docker_volumes. Given that, I think the Docker command you were running was missing the second part of the mount. Try this:

docker run -it -v /home/taherimo/neoantigen_vaccine_pipeline_docker_volumes/inputs:/inputs -v /home/taherimo/neoantigen_vaccine_pipeline_docker_volumes/outputs:/outputs -v /home/taherimo/neoantigen_vaccine_pipeline_docker_volumes/reference-genome:/reference-genome openvax/neoantigen-vaccine-pipeline:latest --configfile=/inputs/idh1_config.yaml

[taherimo]

@julia326 Thanks for your help. I think it is working now.