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DOH-JDJ0303 / vaper

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mv: cannot create directory '/flu-amd/IRMA_RES/modules/zQCNwBiT5rr5T3CiVknW': Permission denied #7

Closed aswarren closed 3 months ago

aswarren commented 3 months ago

Description of the bug

Trying to follow the default invocation nextflow run -profile apptainer -r main --input ./vaper_samplesheet.csv --outdir vaper_results

Makes it to the IRMA step and I consistently get mv: cannot create directory '/flu-amd/IRMA_RES/modules/zQCNwBiT5rr5T3CiVknW': Permission denied

I tried to paper over it by adding a bind to the apptainer portion of the nextflow.config runOptions = '--bind /my_accessible_dir:/flu-amd/IRMA_RES'

and then do the following on the local instance nextflow run ./vaper -profile apptainer --input ./vaper_samplesheet.csv --outdir vaper_results -c ./vaper/nextflow.config

but I still get the same error.

Command used and terminal output

nextflow run -profile apptainer -r main --input ./vaper_samplesheet.csv --outdir vaper_results

Relevant files

No response

System information

No response

DOH-JDJ0303 commented 3 months ago

@aswarren, this should be fixed now. Let me know if the problem persists and I will keep looking into it. Thanks!

aswarren commented 3 months ago

Command error: INFO: gocryptfs not found, will not be able to use gocryptfs mv: cannot create directory '/flu-amd/IRMA_RES/modules/bQTNqegz7CyWT3JU8Dk6': Permission denied

I am still getting this error with the -latest option. Also after pulling down the latest from a local repo. Seems to come primarily from the docker image used for docker not being writeable? Respectively here are the two commands:

nextflow run DOH-JDJ0303/VAPER -profile apptainer -r main -latest --input ./vaper_samplesheet.csv --outdir vaper_results --max_cpus 30 --max_memory 270.GB

nextflow run ./vaper -profile apptainer --input ./vaper_samplesheet.csv --outdir vaper_results --max_cpus 30 --max_memory 270.GB

DOH-JDJ0303 commented 3 months ago

This issue is specific to Singularity/Apptainer. I have noticed that nextflow can be a bit weird about pulling the latest updates from a repo. It may be worth cloning the repo and calling it locally. This should be less of an issue in the future when a stable version is released.

  1. git clone https://github.com/DOH-JDJ0303/vaper.git
  2. run nextflow vaper/main.nf -profile apptainer --input vaper_samplesheet.csv --outdir vaper_results --max_cpus 30 --max_memory 270.GB

If that doesn't work, then I will continue troubleshooting.

DOH-JDJ0303 commented 3 months ago

Sorry, re-reading your comment and you said you tried cloning locally. Are you able to share the .command.run file for the failed run? It will be in the work directory for the failed process (e.g. work/03/190460ecad572c85c11aa21eb6da49/.command.run). It should help confirm that the changes I made were introduced.

aswarren commented 3 months ago

same error with: nextflow run ./vaper/main.nf -profile apptainer --input ./vaper_samplesheet.csv --outdir vaper_results --max_cpus 30 --max_memory 270.GB

git rev-parse HEAD 927edde0e6ed419f3bed94d41e43ba83b6bc2322

Find the .command.run attached. example.command.run.txt

DOH-JDJ0303 commented 3 months ago

Ok, thanks! I will continue testing.

aswarren commented 3 months ago

Guessing here, but --writable-tmpfs wouldn't apply to irma_path=\$(which IRMA)

Since that is located in the staphb container straight up in /flu-amd/ or whatever.

https://github.com/DOH-JDJ0303/vaper/blob/927edde0e6ed419f3bed94d41e43ba83b6bc2322/modules/local/irma.nf#L29

DOH-JDJ0303 commented 3 months ago

Ok. I think I came up with a solution that should be compatible with Singularity/Apptainer. Let me know if the issue still persists.