error running the test

[egenomics]

Hi, I am trying to use sarek in a local workstation. After installing singularity and docker, and pulling the Sarek-test I obtain the following error when I try to execute it:

jl@lynx:/soft/Sarek-test$ nextflow run build.nf --outDir References/smallGRCh37 --refDir Sarek-data/reference --tag latest -profile singularity

N E X T F L O W ~ version 19.10.0 Launching build.nf [sad_boyd] - revision: 4b1f23a848 WARN: Access to undefined parameter verbose -- Initialise it to a default value eg. params.verbose = some_value WARN: Access to undefined parameter containers -- Initialise it to a default value eg. params.containers = some_value

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.' . / ____| | | / |\- \ | ( | | | | \ `-| \ \/ | ´/ | |/ / \ | \ / __) | | | | | < `|__\' |____/_|| \/||\\ Sarek - Workflow For Somatic And Germline Variations ~ 2.3 - 4b1f23a848 Command Line: nextflow run build.nf --outDir References/smallGRCh37 --refDir Sarek-data/reference --tag latest -profile singularity Project Dir : /soft/Sarek-test Launch Dir : /soft/Sarek-test Work Dir : /soft/Sarek-test/work Out Dir : References/smallGRCh37 Genome : smallGRCh37 Containers Repository : docker://maxulysse WARN: Access to undefined parameter containerPath -- Initialise it to a default value eg. params.containerPath = some_value ContainerPath: null Tag : latest [- ] process > BuildWithDocker - [- ] process > PullToSingularity - [- ] process > PushToDocker - [- ] process > DecompressFile - [- ] process > BuildBWAindexes - [- ] process > BuildReferenceIndex - [- ] process > BuildSAMToolsIndex - [- ] process > BuildVCFIndex - [- ] process > BuildCache_snpEff - [- ] process > BuildWithDocker - [- ] process > PullToSingularity - [- ] process > PushToDocker - [- ] process > DecompressFile - [- ] process > BuildBWAindexes - [- ] process > BuildReferenceIndex - [- ] process > BuildSAMToolsIndex - [- ] process > BuildVCFIndex - [- ] process > BuildCache_snpEff - [- ] process > BuildCache_VEP - [- ] process > DownloadCADD - Pulling Singularity image docker://maxulysse/sarek:latest [cache /home/jl/.singularity/maxulysse-sarek-latest.img] N E X T F L O W ~ version 19.10.0 5170 Sarek - Workflow For Somatic And Germline Variations ~ 2.3 - 4b1f23a848 Workflow execution stopped with the following message: null N E X T F L O W ~ version 19.10.0 5170 Sarek - Workflow For Somatic And Germline Variations ~ 2.3 - 4b1f23a848 Command Line: nextflow run build.nf --outDir References/smallGRCh37 --refDir Sarek-data/reference --tag latest -profile singularity Project Dir : /soft/Sarek-test Launch Dir : /soft/Sarek-test Work Dir : /soft/Sarek-test/work Out Dir : References/smallGRCh37 Genome : smallGRCh37 Containers Repository : docker://maxulysse ContainerPath: null Tag : latest Completed at: 2020-01-02T16:33:48.201923+01:00 Duration : 3s Success : false Exit status : null Error report: Error executing process > 'DecompressFile (Mills_and_1000G_gold_standard.indels.b37.small.vcf.gz)'

Caused by: Failed to pull singularity image command: singularity pull --name maxulysse-sarek-latest.img docker://maxulysse/sarek:latest > /dev/null status : 1 message: WARNING: pull for Docker Hub is not guaranteed to produce the WARNING: same image on repeated pull. Use Singularity Registry WARNING: (shub://) to pull exactly equivalent images. ERROR MANIFEST_UNKNOWN: manifest unknown ERROR: pulling container failed! WARN: Access to undefined parameter snpEff_cache -- Initialise it to a default value eg. params.snpEff_cache = some_value WARN: Access to undefined parameter cadd_version -- Initialise it to a default value eg. params.cadd_version = some_value WARN: Access to undefined parameter vep_cache -- Initialise it to a default value eg. params.vep_cache = some_value WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info. Error executing process > 'DecompressFile (Mills_and_1000G_gold_standard.indels.b37.small.vcf.gz)'

Caused by: Failed to pull singularity image command: singularity pull --name maxulysse-sarek-latest.img docker://maxulysse/sarek:latest > /dev/null status : 1 message: WARNING: pull for Docker Hub is not guaranteed to produce the WARNING: same image on repeated pull. Use Singularity Registry WARNING: (shub://) to pull exactly equivalent images. ERROR MANIFEST_UNKNOWN: manifest unknown ERROR: pulling container failed!

If I try to run the command that fails alone:

jl@lynx:/soft/Sarek-test$ singularity pull --name maxulysse-sarek-latest.img docker://maxulysse/sarek:latest WARNING: pull for Docker Hub is not guaranteed to produce the WARNING: same image on repeated pull. Use Singularity Registry WARNING: (shub://) to pull exactly equivalent images. Docker image path: index.docker.io/maxulysse/sarek:latest ERROR MANIFEST_UNKNOWN: manifest unknown Cleaning up... ERROR: pulling container failed!

[maxulysse]

Hi, I'm sorry, I'm on vacation and have a less than reliable connection.

We recently ported sarek to nf-core: https://github.com/nf-core/sarek so I'll recommend you have a look at it. There are lots of improvement.

But if you still want to use this version I'll recommend using --tag 2.3 or 2.3FIX1 instead.

All the best, Maxime

[egenomics]

Hi, Good, I will try that one :) However I have a question, why singularity was prefered before nf-core and now docker is favoured?

Best, JL

[apeltzer]

Hi JL!

the profiles in the nf-core version should load Singularity and pull the Docker Image, giving you the same behaviour. In other words, we only store the Docker Image but users can use both Docker directly or Singularity that can convert the docker image "on-the-fly" to a Singularity container without you noticing 👍

[maxulysse]

@egenomics Any luck with nf-core/sarek?