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connor-lab / ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
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docker profile not working #95

Open rrdavis77 opened 3 years ago

rrdavis77 commented 3 years ago

Trying to run this pipeline with the docker profile on a local linux machine. I am running into an issue with this profile as it seems to not create the proper environment/docker as bwa is not available.

nextflow run connor-lab/ncov2019-artic-nf -profile docker --illumina --prefix TEST --directory /home/ryan/ARTIC_test/ `Error executing process > 'ncovIllumina:prepareReferenceFiles:indexReference (nCoV-2019.reference.fasta)'

Caused by: Process ncovIllumina:prepareReferenceFiles:indexReference (nCoV-2019.reference.fasta) terminated with an error exit status (127)

Command executed:

ln -s nCoV-2019.reference.fasta ref.fa bwa index ref.fa

Command exit status: 127

Command output: (empty)

Command error: .command.sh: line 3: bwa: command not found

Work dir: /home/ryan/ARTIC_test/work/73/2d6da87e9e867405f60c73c124448e

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

I tried the conda profile and it quits without an error.

Thanks for any help!

LaetiGaston commented 3 years ago

Hi, I try the docker profile too and I got exactly the same issue...

Do you solve it? Or do you use an other profile to work?

Thanks for any help too!

rrdavis77 commented 3 years ago

I never got it to work and tried the viralrecon pipeline from the nfcore folks. That has been working great.

Pragungrb commented 2 years ago

I am facing the same issue. Has anyone found a solution to this issue? Any help would be appreciated. Is it related to the docker container not initializing properly?