Installation of nf core deepvariant in cluster

[Priyadarshini Thirunavukkarasu]

Hello, I installed next flow in the computing cluster but I am not able to use the docker files required for running deep variant analysis. I used the following command: nextflow run nf-core/deepvariant -profile test,docker                               


N E X T F L O W  ~  version 21.10.4
Launching `nf-core/deepvariant` [lethal_tesla] - revision: 2b5486356c [master]
Downloading plugin nf-a...@1.3.4
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nf-core/deepvariant v1.0"
=======================================================
Pipeline Name  : nf-core/deepvariant
Pipeline Version: 1.0
Bam file       : https://github.com/nf-core/test-datasets/raw/deepvariant/testdata/NA12878_S1.chr20.10_10p1mb.bam
Bed file       : https://github.com/nf-core/test-datasets/raw/deepvariant/testdata/test_nist.b37_chr20_100kbp_at_10mb.bed
Reference genome: hg19chr20
Fasta Ref      : s3://deepvariant-data/genomes/hg19chr20/chr20.fa
Fasta Index    : s3://deepvariant-data/genomes/hg19chr20/chr20.fa.fai
Fasta gzipped  : s3://deepvariant-data/genomes/hg19chr20/chr20.fa.gz
Fasta gzipped Index: s3://deepvariant-data/genomes/hg19chr20/chr20.fa.gz.fai
Fasta bgzip Index: s3://deepvariant-data/genomes/hg19chr20/chr20.fa.gz.gzi
Max Memory     : 6 GB
Max CPUs       : 2
Max Time       : 2d
Model          : wgs
Output dir     : results
Working dir    : /scicore/home/cichon/thirun0000/my-pipelines/nf-core/deepvariant-master/work
Container Engine: docker
Container      : nfcore/deepvariant:1.0
Current home   : /scicore/home/cichon/thirun0000
Current user   : thirun0000
Current path   : /scicore/home/cichon/thirun0000/my-pipelines/nf-core/deepvariant-master
Script dir     : /scicore/home/cichon/thirun0000/.nextflow/assets/nf-core/deepvariant
Config Profile : test,docker
=========================================
executor >  local (1)
[-        ] process > preprocess_bam        -
[-        ] process > make_examples         -
[-        ] process > call_variants         -
[-        ] process > postprocess_variants  -
[e7/dec5cb] process > get_software_versions [100%] 1 of 1, failed: 1 ✘
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'get_software_versions'

Caused by:
  Process `get_software_versions` terminated with an error exit status (127)

Command executed:

  echo 1.0 &> v_nf_deepvariant.txt
  echo 21.10.4 &> v_nextflow.txt
  ls /opt/conda/pkgs/ &> v_deepvariant.txt
  python --version &> v_python.txt
  pip --version &> v_pip.txt
  samtools --version &> v_samtools.txt
  lbzip2 --version &> v_lbzip2.txt
  bzip2 --version &> v_bzip2.txt
  scrape_software_versions.py &> software_versions_mqc.yaml

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.run: line 279: docker: command not found

Work dir:
  /scicore/home/cichon/thirun0000/my-pipelines/nf-core/deepvariant-master/work/e7/dec5cbd65b63e4fdd5ccced4f1e516

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`


Fastagz file not found: s3://deepvariant-data/genomes/hg19chr20/chr20.fa.gz


Fai file not found: s3://deepvariant-data/genomes/hg19chr20/chr20.fa.fai


gzfai file not found: s3://deepvariant-data/genomes/hg19chr20/chr20.fa.gz.fai


please specify --bed option (--bed bedfile)


https://github.com/nf-core/test-datasets/raw/deepvariant/testdata/NA12878_S1.chr20.10_10p1mb.bam not found


gzi file not found: s3://deepvariant-data/genomes/hg19chr20/chr20.fa.gz.gzi

[Paolo Di Tommaso]

Hello, 

Please consider submitting this question on nf-core channels https://nf-co.re/join

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[Alan Hoyle]

That looks to me like you might not have Docker installed on your cluster, or you're trying to execute the Nextflow process from the command line of your cluster's login node, which often wouldn't have Docker installed.  

As an aside, the S3 integration is really neat and this inspired me to test it.  I made a one-liner s3test.nf, and I was able to print a public file from there really easily, without setting up any kind of special credentials:

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  -  Alan Hoyle  -  al...@alanhoyle.com  -  http://www.alanhoyle.com/  -

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