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Arcadia-Science / noveltree

NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.
GNU Affero General Public License v3.0
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Error executing process > 'NOVELTREE:INPUT_CHECK:SAMPLESHEET_CHECK (tsar_downsamp_test_samplesheet.csv)' #96

Open bioinfowheat opened 1 year ago

bioinfowheat commented 1 year ago

Description of the bug

am trying to get noveltree to run on my server. have nextflow and dockter installed running nextflow within downloaded folder from github

get the error below

Command used and terminal output

./nextflow run . -profile docker -params-file https://github.com/Arcadia-Science/test-datasets/raw/main/noveltree/tsar_downsamp_test_parameters.json
N E X T F L O W  ~  version 23.10.0
Launching `./main.nf` [extravagant_dubinsky] DSL2 - revision: 9c56f835c6

WARN: Found unexpected parameters:
* --config_profile_name: null
* --config_profile_url: null
* --config_profile_contact: null
* --config_profile_description: null
* --custom_config_base: https://raw.githubusercontent.com/nf-core/configs/master
* --custom_config_version: master
* --download_annots: minimal
- Ignore this warning: params.schema_ignore_params = "config_profile_name,config_profile_url,config_profile_contact,config_profile_description,custom_config_base,custom_config_version,download_annots" 

------------------------------------------------------
  Arcadia-Science/noveltree v1.0.0-alpha
------------------------------------------------------
Core Nextflow options
  runName                 : extravagant_dubinsky
  containerEngine         : docker
  launchDir               : /mnt/griffin/chrwhe/software/noveltree-1.0.1-alpha
  workDir                 : /mnt/griffin/chrwhe/software/noveltree-1.0.1-alpha/work
  projectDir              : /mnt/griffin/chrwhe/software/noveltree-1.0.1-alpha
  userName                : chrwhe
  profile                 : docker
  configFiles             : /mnt/griffin/chrwhe/software/noveltree-1.0.1-alpha/nextflow.config

Input/output options
  input                   : https://github.com/Arcadia-Science/test-datasets/raw/main/noveltree/tsar_downsamp_test_samplesheet.csv
  mcl_inflation           : 1.25,3.75,5.25,6.75,8.25
  outdir                  : results-tsar-downsamp-test
  min_prop_spp_for_spptree: 0.75
  min_num_grp_per_og      : 2
  max_copy_num_spp_tree   : 3
  max_copy_num_gene_trees : 5

Max job request options
  max_cpus                : 72

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use Arcadia-Science/noveltree for your analysis please cite:

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/Arcadia-Science/noveltree/blob/master/CITATIONS.md
------------------------------------------------------
executor >  local (6)
[93/b1da97] process > NOVELTREE:INPUT_CHECK:SAMPLESHEET_CHECK (tsar_downsamp_test_samplesheet.csv) [ 83%] 5 of 6, failed: 5, retries: 5
[-        ] process > NOVELTREE:ANNOTATE_UNIPROT                                                   -
[-        ] process > NOVELTREE:ORTHOFINDER_PREP_TEST                                              -
[-        ] process > NOVELTREE:DIAMOND_BLASTP_TEST                                                -
[-        ] process > NOVELTREE:ORTHOFINDER_MCL_TEST                                               -
executor >  local (6)
[93/b1da97] process > NOVELTREE:INPUT_CHECK:SAMPLESHEET_CHECK (tsar_downsamp_test_samplesheet.csv) [100%] 6 of 6, failed: 6, retries: 5 ✘
[-        ] process > NOVELTREE:ANNOTATE_UNIPROT                                                   -
[-        ] process > NOVELTREE:ORTHOFINDER_PREP_TEST                                              -
[-        ] process > NOVELTREE:DIAMOND_BLASTP_TEST                                                -
[-        ] process > NOVELTREE:ORTHOFINDER_MCL_TEST                                               -
[-        ] process > NOVELTREE:COGEQC                                                             -
[-        ] process > NOVELTREE:SELECT_INFLATION                                                   -
[-        ] process > NOVELTREE:BUSCO_SHALLOW                                                      -
[-        ] process > NOVELTREE:BUSCO_BROAD                                                        -
[-        ] process > NOVELTREE:ORTHOFINDER_PREP_ALL                                               -
[-        ] process > NOVELTREE:DIAMOND_BLASTP_ALL                                                 -
[-        ] process > NOVELTREE:ORTHOFINDER_MCL_ALL                                                -
[-        ] process > NOVELTREE:FILTER_ORTHOGROUPS                                                 -
[-        ] process > NOVELTREE:ALIGN_SEQS                                                         -
[-        ] process > NOVELTREE:ALIGN_REMAINING_SEQS                                               -
[-        ] process > NOVELTREE:INFER_TREES                                                        -
[-        ] process > NOVELTREE:INFER_REMAINING_TREES                                              -
[-        ] process > NOVELTREE:ASTEROID                                                           -
[-        ] process > NOVELTREE:SPECIESRAX                                                         -
[-        ] process > NOVELTREE:GENERAX_PER_FAMILY                                                 -
[-        ] process > NOVELTREE:GENERAX_PER_SPECIES                                                -
[-        ] process > NOVELTREE:ORTHOFINDER_PHYLOHOGS                                              -
[27/3c9d4d] NOTE: Process `NOVELTREE:INPUT_CHECK:SAMPLESHEET_CHECK (tsar_downsamp_test_samplesheet.csv)` terminated with an error exit status (126) -- Execution is retried (1)
[3d/20363a] NOTE: Process `NOVELTREE:INPUT_CHECK:SAMPLESHEET_CHECK (tsar_downsamp_test_samplesheet.csv)` terminated with an error exit status (126) -- Execution is retried (2)
[ed/35e7cc] NOTE: Process `NOVELTREE:INPUT_CHECK:SAMPLESHEET_CHECK (tsar_downsamp_test_samplesheet.csv)` terminated with an error exit status (126) -- Execution is retried (3)
[f9/7bd1ba] NOTE: Process `NOVELTREE:INPUT_CHECK:SAMPLESHEET_CHECK (tsar_downsamp_test_samplesheet.csv)` terminated with an error exit status (126) -- Execution is retried (4)
[a1/950f1c] NOTE: Process `NOVELTREE:INPUT_CHECK:SAMPLESHEET_CHECK (tsar_downsamp_test_samplesheet.csv)` terminated with an error exit status (126) -- Execution is retried (5)
ERROR ~ Error executing process > 'NOVELTREE:INPUT_CHECK:SAMPLESHEET_CHECK (tsar_downsamp_test_samplesheet.csv)'

Caused by:
  Process `NOVELTREE:INPUT_CHECK:SAMPLESHEET_CHECK (tsar_downsamp_test_samplesheet.csv)` terminated with an error exit status (126)

Command executed:

  check_samplesheet.py \
      tsar_downsamp_test_samplesheet.csv \
      complete_samplesheet.valid.csv

  cat <<-END_VERSIONS > versions.yml
  "NOVELTREE:INPUT_CHECK:SAMPLESHEET_CHECK":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  docker: Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post http://%2Fvar%2Frun%2Fdocker.sock/v1.39/containers/create?name=nxf-AH6jSZP4TGrKmpIpbJvcSgLz: dial unix /var/run/docker.sock: connect: permission denied.
  See 'docker run --help'.

Work dir:
  /mnt/griffin/chrwhe/software/noveltree-1.0.1-alpha/work/93/b1da971f5a7315f07b55a641cc08f4

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details

Relevant files

No response

System information

No response

austinhpatton commented 9 months ago

Apologies for not catching this sooner! It seems the nature of the error you've run into has to do with permissions related to docker.

docker: Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post http://%2Fvar%2Frun%2Fdocker.sock/v1.39/containers/create?name=nxf-AH6jSZP4TGrKmpIpbJvcSgLz: dial unix /var/run/docker.sock: connect: permission denied.

Without being able to see .nextflow.log, I'd suspect a couple possible sources of the error, especially since you say you're trying to run NovelTree on a server:

  1. Your user is not added to the docker group. Can try running sudo usermod -aG docker $USER to fix this.
  2. You can try restarting the docker service using sudo systemctl restart docker or try starting it with sudo systemctl start docker

As a simple test, you could check to see whether your docker is installed, configured correctly, and running using docker run hello-world.

If these fail, could you post the output of .nextflow.log for the failed run after attempting these fixes?

Thanks!