Error executing process > 'NOVELTREE:INPUT_CHECK:SAMPLESHEET_CHECK (tsar_downsamp_test_samplesheet.csv)'
bioinfowheat opened this issue · comments
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 detailsRelevant files
No response
System information
No response
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:
- Your user is not added to the docker group. Can try running
sudo usermod -aG docker $USERto fix this. - You can try restarting the docker service using
sudo systemctl restart dockeror try starting it withsudo 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!