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funcscan -profile test failed #414

Closed
asogg opened this issue Sep 2, 2024 · 2 comments
Closed

funcscan -profile test failed #414

asogg opened this issue Sep 2, 2024 · 2 comments
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bug Something isn't working

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@asogg
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asogg commented Sep 2, 2024

Description of the bug

Dear funcscan team,
your pipeline is very interesting and i tried to run the test but it stopped very early due to some errors.
i attach the terminal command and the output below.
best regards
Alessio

Command used and terminal output

as@as:~/nextflow$  nextflow run nf-core/funcscan -profile test --outdir /home/as/test

 N E X T F L O W   ~  version 24.04.4

Pulling nf-core/funcscan ...
 downloaded from https://github.com/nf-core/funcscan.git
Launching `https://github.com/nf-core/funcscan` [lonely_hodgkin] DSL2 - revision: 571d7eb6dd [master]

Downloading plugin [email protected]


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/funcscan v2.0.0-g571d7eb
------------------------------------------------------
Core Nextflow options
  revision                         : master
  runName                          : lonely_hodgkin
  launchDir                        : /home/as/nextflow
  workDir                          : /home/as/nextflow/work
  projectDir                       : /home/as/.nextflow/assets/nf-core/funcscan
  userName                         : as
  profile                          : test
  configFiles                      : 

Input/output options
  input                            : https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet_reduced.csv
  outdir                           : /home/as/test

Screening type activation
  run_amp_screening                : true
  run_arg_screening                : true

AMP: hmmsearch
  amp_run_hmmsearch                : true
  amp_hmmsearch_models             : https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/hmms/mybacteriocin.hmm

AMP: ampcombi2 parsetables
  amp_ampcombi_parsetables_dbevalue: 5

AMP: ampcombi2 cluster
  amp_ampcombi_cluster_covmode     : 0
  amp_ampcombi_cluster_mode        : 1

ARG: AMRFinderPlus
  arg_amrfinderplus_identmin       : -1

ARG: fARGene
  arg_fargene_hmmmodel             : class_a,class_b_1_2

Institutional config options
  config_profile_name              : AMP/ARG Pyrodigal test profile
  config_profile_description       : Minimal test dataset to check pipeline function

Max job request options
  max_cpus                         : 2
  max_memory                       : 8.GB
  max_time                         : 6.h

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/funcscan for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.7643099

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

* Software dependencies
  https://github.com/nf-core/funcscan/blob/master/CITATIONS.md
------------------------------------------------------
executor >  local (3)
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:GUNZIP_INPUT_PREP                 -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:PYRODIGAL              -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_FAA   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_FNA   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_GBK   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPLIFY_PREDICT               -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:MACREL_CONTIGS                -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:GUNZIP_MACREL_PRED            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:GUNZIP_MACREL_ORFS            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPIR                         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMP_HMMER_HMMSEARCH           -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMP_GUNZIP_HMMER_HMMSEARCH    -
[c2/6f4c41] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:DRAMP_DOWNLOAD                [  0%] 0 of 1
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_PARSETABLES         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_COMPLETE            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_CLUSTER             -
[2c/de1eb5] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update) [  0%] 0 of 1
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_RUN             -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_AMRFINDERPLUS   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:ARGNORM_AMRFINDERPLUS         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:FARGENE                       -
executor >  local (3)
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:GUNZIP_INPUT_PREP                 -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:PYRODIGAL              -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_FAA   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_FNA   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_GBK   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPLIFY_PREDICT               -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:MACREL_CONTIGS                -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:GUNZIP_MACREL_PRED            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:GUNZIP_MACREL_ORFS            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPIR                         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMP_HMMER_HMMSEARCH           -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMP_GUNZIP_HMMER_HMMSEARCH    -
[c2/6f4c41] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:DRAMP_DOWNLOAD                [  0%] 0 of 1
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_PARSETABLES         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_COMPLETE            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_CLUSTER             -
[2c/de1eb5] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update) [  0%] 0 of 1
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_RUN             -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_AMRFINDERPLUS   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:ARGNORM_AMRFINDERPLUS         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:FARGENE                       -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_FARGENE         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:UNTAR_CARD                    -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:RGI_CARDANNOTATION            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:RGI_MAIN                      -
executor >  local (3)
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:GUNZIP_INPUT_PREP                 -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:PYRODIGAL              -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_FAA   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_FNA   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_GBK   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPLIFY_PREDICT               -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:MACREL_CONTIGS                -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:GUNZIP_MACREL_PRED            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:GUNZIP_MACREL_ORFS            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPIR                         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMP_HMMER_HMMSEARCH           -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMP_GUNZIP_HMMER_HMMSEARCH    -
[c2/6f4c41] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:DRAMP_DOWNLOAD                [  0%] 0 of 1
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_PARSETABLES         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_COMPLETE            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_CLUSTER             -
[2c/de1eb5] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update) [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_RUN             -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_AMRFINDERPLUS   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:ARGNORM_AMRFINDERPLUS         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:FARGENE                       -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_FARGENE         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:UNTAR_CARD                    -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:RGI_CARDANNOTATION            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:RGI_MAIN                      -
executor >  local (3)
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:GUNZIP_INPUT_PREP                 [  0%] 0 of 2
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:PYRODIGAL              -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_FAA   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_FNA   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_GBK   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPLIFY_PREDICT               -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:MACREL_CONTIGS                -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:GUNZIP_MACREL_PRED            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:GUNZIP_MACREL_ORFS            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPIR                         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMP_HMMER_HMMSEARCH           -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMP_GUNZIP_HMMER_HMMSEARCH    -
[c2/6f4c41] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:DRAMP_DOWNLOAD                [  0%] 0 of 1
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_PARSETABLES         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_COMPLETE            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_CLUSTER             -
[2c/de1eb5] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update) [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_RUN             -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_AMRFINDERPLUS   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:ARGNORM_AMRFINDERPLUS         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:FARGENE                       -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_FARGENE         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:UNTAR_CARD                    -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:RGI_CARDANNOTATION            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:RGI_MAIN                      -
executor >  local (3)
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:GUNZIP_INPUT_PREP                 [  0%] 0 of 2
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:PYRODIGAL              -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_FAA   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_FNA   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_GBK   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPLIFY_PREDICT               -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:MACREL_CONTIGS                -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:GUNZIP_MACREL_PRED            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:GUNZIP_MACREL_ORFS            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPIR                         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMP_HMMER_HMMSEARCH           -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMP_GUNZIP_HMMER_HMMSEARCH    -
[c2/6f4c41] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:DRAMP_DOWNLOAD                [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_PARSETABLES         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_COMPLETE            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_CLUSTER             -
[2c/de1eb5] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update) [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_RUN             -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_AMRFINDERPLUS   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:ARGNORM_AMRFINDERPLUS         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:FARGENE                       -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_FARGENE         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:UNTAR_CARD                    -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:RGI_CARDANNOTATION            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:RGI_MAIN                      -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_RGI             -
executor >  local (3)
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:GUNZIP_INPUT_PREP                 [  0%] 0 of 2
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:PYRODIGAL              -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_FAA   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_FNA   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_GBK   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPLIFY_PREDICT               -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:MACREL_CONTIGS                -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:GUNZIP_MACREL_PRED            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:GUNZIP_MACREL_ORFS            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPIR                         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMP_HMMER_HMMSEARCH           -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMP_GUNZIP_HMMER_HMMSEARCH    -
[c2/6f4c41] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:DRAMP_DOWNLOAD                [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_PARSETABLES         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_COMPLETE            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_CLUSTER             -
[2c/de1eb5] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update) [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_RUN             -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_AMRFINDERPLUS   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:ARGNORM_AMRFINDERPLUS         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:FARGENE                       -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_FARGENE         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:UNTAR_CARD                    [  0%] 0 of 1
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:RGI_CARDANNOTATION            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:RGI_MAIN                      -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_RGI             -
executor >  local (3)
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:GUNZIP_INPUT_PREP                 [  0%] 0 of 2
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:PYRODIGAL              -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_FAA   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_FNA   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_GBK   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPLIFY_PREDICT               -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:MACREL_CONTIGS                -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:GUNZIP_MACREL_PRED            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:GUNZIP_MACREL_ORFS            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPIR                         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMP_HMMER_HMMSEARCH           -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMP_GUNZIP_HMMER_HMMSEARCH    -
[c2/6f4c41] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:DRAMP_DOWNLOAD                [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_PARSETABLES         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_COMPLETE            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_CLUSTER             -
[2c/de1eb5] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update) [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_RUN             -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_AMRFINDERPLUS   -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:ARGNORM_AMRFINDERPLUS         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:FARGENE                       -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_FARGENE         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:UNTAR_CARD                    [  0%] 0 of 1
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:RGI_CARDANNOTATION            -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:RGI_MAIN                      -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_RGI             -
[0e/b25523] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:DEEPARG_DOWNLOADDATA          [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:DEEPARG_PREDICT               -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_DEEPARG         -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:ARGNORM_DEEPARG               -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:ABRICATE_RUN                  -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_ABRICATE        -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:ARGNORM_ABRICATE              -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_SUMMARIZE       -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:MULTIQC                           -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/funcscan] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:ARG:DEEPARG_DOWNLOADDATA'

Caused by:
  Process `NFCORE_FUNCSCAN:FUNCSCAN:ARG:DEEPARG_DOWNLOADDATA` terminated with an error exit status (127)


Command executed:

  # Theano needs a writable space and uses the home directory by default,
  # but the latter is not always writable, for instance when Singularity
  # is run in --no-home mode
  mkdir -p theano
  export THEANO_FLAGS="base_compiledir=$PWD/theano"
  
  deeparg \
      download_data \
       \
      -o db/
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FUNCSCAN:FUNCSCAN:ARG:DEEPARG_DOWNLOADDATA":
      deeparg: 1.0.4
  END_VERSIONS

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 9: deeparg: command not found

Work dir:
  /home/as/nextflow/work/0e/b255237544eebd61f7e43547da450d

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

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

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

Relevant files

.nextflow.log

System information

nextflow version 24.04.4
local workstation
executor terminal
os Ubuntu 20.04.6 LTS
https://github.com/nf-core/funcscan` [lonely_hodgkin] DSL2 - revision: 571d7eb [master]
@asogg asogg added the bug Something isn't working label Sep 2, 2024
@jfy133
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jfy133 commented Sep 3, 2024

Hi @asogg you need to specify where to get the software from:

nextflow run nf-core/funcscan -profile test --outdir /home/as/test

needs to be soemthing like

nextflow run nf-core/funcscan -profile test,docker --outdir /home/as/test

or

nextflow run nf-core/funcscan -profile test,conda --outdir /home/as/test

etc.

Please check the usage documentation page:

https://nf-co.re/funcscan/1.1.6/docs/usage/#core-nextflow-arguments

@jfy133
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jfy133 commented Sep 3, 2024

And also here might help: https://nf-co.re/docs/usage/getting_started/installation

@jfy133 jfy133 closed this as completed Sep 3, 2024
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@asogg @jfy133