Nextflow failed to deploy a container

[chenfengMeng]

Bug report

When I trying to deploy a container called "quay.io/wtsicgp/cgp-telomerehunter:1.1.0", it failed to deploy it on google cloud even if I don't run any command. but when I run it locally, it work successfully.

Expected behavior and actual behavior

It should return some success result.

Steps to reproduce the problem

process Telomerehunter {
container "quay.io/wtsicgp/cgp-telomerehunter:1.1.0"
disk 50 gb

script
"""
"""
}

Program output

Error executing process > 'Telomerehunter'

Caused by:
Process Telomerehunter terminated with an error exit status (9)

Command executed:

Command exit status:
9

Command output:
(empty)

Command error:
Execution failed: generic::failed_precondition: while running "nf-5665840d56f2d3211a53347091a50bf2-main": unexpected exit status 1 was not ignored

Work dir:
gs://repare-nextflow-work/work_dir/56/65840d56f2d3211a53347091a50bf2

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

[mribeirodantas]

Hello, @chenfengMeng!

1. How you're using Google Cloud? Google Life Sciences? Google Cloud Batch?
2. Can you share a minimal reproducible example?

[chenfengMeng]

Thanks for your fast reply, We are using google life sciences. this is the setting of my GCP,
process.executor = "google-lifesciences"
workDir = "gs://someplace/work_dir"
google.location = "us-central1"
google.region = "us-central1"
google.project = "your-project"

[chenfengMeng]

the minimum reproducible example:
### show.nf:

nextflow.enable.dsl=1
params.outdir                             = false        //the path to the output directory


process Telomerehunter {
        // primarily take from nf-core sarez

        container "quay.io/wtsicgp/cgp-telomerehunter:1.1.0"
        containerOptions "--user root"

        disk 50.GB

        script:
        """
        touch *.bai
        touch *.bam
        """
}

[chenfengMeng]

##show.config

docker{
    enabled = true
}
profiles {
  gcp {
       	process.executor = "google-lifesciences"
       	workDir          = "gs://someplace/work_dir"
       	google.project   = "your project"
	google.region    = "us-central1"
  }
  localRef {
        path_to_refs              = "." //"[/path/to/refs]"
        params.ref_genome         = "${path_to_refs}/dnaseq/hg19/invitae/hg19.fa"
        params.ref_genome_index   = "${path_to_refs}/dnaseq/hg19/invitae/hg19.fa.fai"
        params.ref_genome_dict    = "${path_to_refs}/dnaseq/hg19/invitae/hg19.fa.dict"
  }
}


process {
	cpu = 1
	memory = 5.GB
}

Notice you may want to customize the project and work directory under your preferred.

[mribeirodantas]

Is there any reason you must use GLS instead of Google Batch? A lot of issues have been solved by using the latter

[mribeirodantas]

This seems to be a problem with the container image. See this issue: nf-core/rnaseq#764

[chenfengMeng]

Thanks for your reply and instruction! and May I know what kind of image has this problem? I mean, this image works just fine in my local computer, but, when I deploy it in google cloud, it broken as a result.

[mribeirodantas]

I'm sorry but I'm not aware of what issue this container image has. I just found the discussion where the container image was identified as the issue.

[ptn24]

@chenfengMeng : Did you ever figure out what the problem was? I think I have the same problem.

[chenfengMeng]

I just created a new docker by myself, it should be the problem of administrator accessibility in the docker, check the layer of the docker construction.

…

On Sun, Dec 24, 2023 at 9:49 PM Peter Nguyen ***@***.***> wrote: @chenfengMeng <https://github.com/chenfengMeng> : Did you ever figure out what the problem was? I think I have the same problem. — Reply to this email directly, view it on GitHub <#3717 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A5QLCGX5VVAQAFMNNMG4YGDYLDSR5AVCNFSM6AAAAAAVPL4U3CVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM3TSNBQHA2TC> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[ptn24]

I see. Can you elaborate on what lines you added to get the image to work? I also have a custom image, but I am not sure where to begin.

[chenfengMeng]

I don't know, I just rebuilt one and then it worked.

…

On Mon, Dec 25, 2023 at 12:47 AM Peter Nguyen ***@***.***> wrote: I see. Can you elaborate on what lines you added to get the image to work? I also have a custom image, but I am not sure where to begin. — Reply to this email directly, view it on GitHub <#3717 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A5QLCGTWPRKB367CGLRVYTTYLEHOVAVCNFSM6AAAAAAVPL4U3CVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM3TSNBRHA4DI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[ptn24]

I see. Thank you!