CODEWITHSUNDEEP
imagesingularity-containernextflowsamtools
sara777
sara777

Reputation: 1

Singularity could not open image

I ran my workflow with nextflow using singularity, for my first process there are no problems, but the second one gives me this error: could not open image /staphb/samtools:1.15.img: failed to retrieve path for /staphb/samtools:1.15.img: lstat /staphb: no such file or directory

This is part of my nextflow.config file:

singularity {
        autoMounts = true
        runOptions = "--bind ${params.bind_path}"
}


singularity.enabled = true

process {
        errorStrategy = "ignore"
        withName:MAP { container = "winnowmap:2.03--h43eeafb_2" }
        withName:SAMTOOLS { container = "/work/my_singularity_container/staphb-samtools-1.15.img" }
     
}


dag { enabled = true }
report { enabled = true }
timeline { enabled = true }
trace { enabled = true }

First I tried changing the container name in my config like this:

withName:SAMTOOLS { container = "staphb/samtools:1.15" }

but it kept giving the same error, so I tried downloading another image, but it still gave me the error:

could not open image /staphb/samtools:1.15.img: failed to retrieve path for /staphb/samtools:1.15.img: lstat /staphb: no such file or directory, even if I changed the container in my nextflow.config:

process {
        errorStrategy = "ignore"
        withName:MAP { container = "winnowmap:2.03--h43eeafb_2" }
        withName:SAMTOOLS { container = "samtools_1.17:hd87286a_1" }

I checked the images and they all work

Can you please help me?

Upvotes: 0

Views: 713

Answers (1)

sara777
sara777

Reputation: 1

I changed the name of my process and workflow and it worked.

Upvotes: 0

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