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Amrfinderplus_update not working in test run #328

Closed
pdy1084 opened this issue Jan 3, 2024 · 4 comments
Closed

Amrfinderplus_update not working in test run #328

pdy1084 opened this issue Jan 3, 2024 · 4 comments
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@jasmezz
Labels
bug Something isn't working
Milestone
2.0 - Brazilian E...

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@pdy1084
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pdy1084 commented Jan 3, 2024

Description of the bug

When I run the nf-core/funcscan pipeline with test,singularity as -profile, Amrfinderplus_update does not work properly and the pipeline crashes.

I could run nf-core/mag in the same HPC before and this worked properly.

Command used and terminal output

------------------Run

$ nextflow run nf-core/funcscan -r 1.1.4 \
         --outdir /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/ \
         -profile test,singularity

------------------Error

... I copy the last lines of the stdout file (which I think are more relevant)

executor >  local (40)
[d9/29f632] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[5a/67ad25] process > NFCORE_FUNCSCAN:FUNCSCAN:BI... [100%] 2 of 2 ✔
[ed/0e6003] process > NFCORE_FUNCSCAN:FUNCSCAN:PR... [100%] 2 of 2 ✔
[9f/edc837] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[d3/f90d15] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[77/d7b476] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[0f/eb4a0a] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[40/93a62d] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[19/cf0ff8] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[ee/aafa74] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[51/141f0f] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 1 of 1 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[f4/4a82ef] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [  0%] 0 of 1
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[c8/300eca] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 4 of 4 ✔
[74/b034ce] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 8 of 8 ✔
[33/b78323] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [  0%] 0 of 2
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[e3/a94b87] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 2 of 2 ✔
[82/de50f2] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:CU... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:MU... -
Pulling Singularity image https://depot.galaxyproject.org/singularity/r-ampir:1.1.0 [cache /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/singularity/depot.galaxyproject.org-singularity-r-ampir-1.1.0.img]
Pulling Singularity image https://depot.galaxyproject.org/singularity/amplify:1.1.0--hdfd78af_0 [cache /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/singularity/depot.galaxyproject.org-singularity-amplify-1.1.0--hdfd78af_0.img]
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location
ERROR ~ Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update)'

Caused by:
  Process `NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update)` terminated with an error exit status (1)

Command executed:

  amrfinder_update -d amrfinderdb
  tar czvf amrfinderdb.tar.gz -C amrfinderdb/$(readlink amrfinderdb/latest) ./

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE":
      amrfinderplus: $(amrfinder --version)
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  Running: amrfinder_update -d amrfinderdb
  Looking up the published databases at https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/
  Looking for the target directory amrfinderdb/2023-11-15.1/
  Downloading AMRFinder database version 2023-11-15.1 into 'amrfinderdb/2023-11-15.1/'
  Running: /usr/local/bin/amrfinder_index amrfinderdb/2023-11-15.1/
  Indexing

  *** ERROR ***
  '/usr/local/bin/makeblastdb'  -in /tmp/amrfinder_index.Ylmgta/db/AMRProt  -dbtype prot  -logfile /tmp/amrfinder_index.Ylmgta/makeblastdb.AMRProt
  status = 135
  Building a new DB, current time: 01/03/2024 15:27:42
  New DB name:   /tmp/amrfinder_index.Ylmgta/db/AMRProt
  New DB title:  /tmp/amrfinder_index.Ylmgta/db/AMRProt
  Sequence type: Protein
  Keep MBits: T
  Maximum file size: 3000000000B

  HOSTNAME: ?
  SHELL: ?
  PWD: /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359
  PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/pdy23/.nextflow/assets/nf-core/funcscan/bin
  Progam name:  amrfinder_index
  Command line: /usr/local/bin/amrfinder_index amrfinderdb/2023-11-15.1/

  *** ERROR ***
  '/usr/local/bin/amrfinder_index' 'amrfinderdb/2023-11-15.1/' > /tmp/amrfinder_update.FoQYnY/amrfinder_index.err
  status = 256


  HOSTNAME: ?
  SHELL: ?
  PWD: /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359
  PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/pdy23/.nextflow/assets/nf-core/funcscan/bin
  Progam name:  amrfinder_update
  Command line: amrfinder_update -d amrfinderdb

Work dir:
  /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

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

executor >  local (40)
[d9/29f632] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[5a/67ad25] process > NFCORE_FUNCSCAN:FUNCSCAN:BI... [100%] 2 of 2 ✔
[ed/0e6003] process > NFCORE_FUNCSCAN:FUNCSCAN:PR... [100%] 2 of 2 ✔
[9f/edc837] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[d3/f90d15] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[77/d7b476] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[0f/eb4a0a] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[40/93a62d] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[19/cf0ff8] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[ee/aafa74] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[51/141f0f] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 1 of 1 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[f4/4a82ef] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[c8/300eca] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 4 of 4 ✔
[74/b034ce] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 8 of 8 ✔
[33/b78323] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [  0%] 0 of 2
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[e3/a94b87] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 2 of 2 ✔
[82/de50f2] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:CU... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:MU... -
Pulling Singularity image https://depot.galaxyproject.org/singularity/r-ampir:1.1.0 [cache /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/singularity/depot.galaxyproject.org-singularity-r-ampir-1.1.0.img]
Pulling Singularity image https://depot.galaxyproject.org/singularity/amplify:1.1.0--hdfd78af_0 [cache /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/singularity/depot.galaxyproject.org-singularity-amplify-1.1.0--hdfd78af_0.img]
Execution cancelled -- Finishing pending tasks before exit
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location
ERROR ~ Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update)'

Caused by:
  Process `NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update)` terminated with an error exit status (1)

Command executed:

  amrfinder_update -d amrfinderdb
  tar czvf amrfinderdb.tar.gz -C amrfinderdb/$(readlink amrfinderdb/latest) ./

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE":
      amrfinderplus: $(amrfinder --version)
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  Running: amrfinder_update -d amrfinderdb
  Looking up the published databases at https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/
  Looking for the target directory amrfinderdb/2023-11-15.1/
  Downloading AMRFinder database version 2023-11-15.1 into 'amrfinderdb/2023-11-15.1/'
  Running: /usr/local/bin/amrfinder_index amrfinderdb/2023-11-15.1/
  Indexing

  *** ERROR ***
  '/usr/local/bin/makeblastdb'  -in /tmp/amrfinder_index.Ylmgta/db/AMRProt  -dbtype prot  -logfile /tmp/amrfinder_index.Ylmgta/makeblastdb.AMRProt
  status = 135
  Building a new DB, current time: 01/03/2024 15:27:42
  New DB name:   /tmp/amrfinder_index.Ylmgta/db/AMRProt
  New DB title:  /tmp/amrfinder_index.Ylmgta/db/AMRProt
  Sequence type: Protein
  Keep MBits: T
  Maximum file size: 3000000000B

  HOSTNAME: ?
  SHELL: ?
  PWD: /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359
  PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/pdy23/.nextflow/assets/nf-core/funcscan/bin
  Progam name:  amrfinder_index
  Command line: /usr/local/bin/amrfinder_index amrfinderdb/2023-11-15.1/

  *** ERROR ***
  '/usr/local/bin/amrfinder_index' 'amrfinderdb/2023-11-15.1/' > /tmp/amrfinder_update.FoQYnY/amrfinder_index.err
  status = 256


  HOSTNAME: ?
  SHELL: ?
  PWD: /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359
  PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/pdy23/.nextflow/assets/nf-core/funcscan/bin
  Progam name:  amrfinder_update
  Command line: amrfinder_update -d amrfinderdb

Work dir:
  /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

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

executor >  local (40)
[d9/29f632] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[5a/67ad25] process > NFCORE_FUNCSCAN:FUNCSCAN:BI... [100%] 2 of 2 ✔
[ed/0e6003] process > NFCORE_FUNCSCAN:FUNCSCAN:PR... [100%] 2 of 2 ✔
[9f/edc837] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[d3/f90d15] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[77/d7b476] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[0f/eb4a0a] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[40/93a62d] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[19/cf0ff8] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[ee/aafa74] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[51/141f0f] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 1 of 1 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[f4/4a82ef] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[c8/300eca] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 4 of 4 ✔
[74/b034ce] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 8 of 8 ✔
[ef/1f456a] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [ 50%] 1 of 2
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[e3/a94b87] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 2 of 2 ✔
[82/de50f2] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:CU... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:MU... -
Execution cancelled -- Finishing pending tasks before exit



ERROR ~ Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update)'

Caused by:
  Process `NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update)` terminated with an error exit status (1)

Command executed:

  amrfinder_update -d amrfinderdb
  tar czvf amrfinderdb.tar.gz -C amrfinderdb/$(readlink amrfinderdb/latest) ./

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE":
      amrfinderplus: $(amrfinder --version)
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  Running: amrfinder_update -d amrfinderdb
  Looking up the published databases at https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/
  Looking for the target directory amrfinderdb/2023-11-15.1/
  Downloading AMRFinder database version 2023-11-15.1 into 'amrfinderdb/2023-11-15.1/'
  Running: /usr/local/bin/amrfinder_index amrfinderdb/2023-11-15.1/
  Indexing

  *** ERROR ***
  '/usr/local/bin/makeblastdb'  -in /tmp/amrfinder_index.Ylmgta/db/AMRProt  -dbtype prot  -logfile /tmp/amrfinder_index.Ylmgta/makeblastdb.AMRProt
  status = 135
  Building a new DB, current time: 01/03/2024 15:27:42
  New DB name:   /tmp/amrfinder_index.Ylmgta/db/AMRProt
  New DB title:  /tmp/amrfinder_index.Ylmgta/db/AMRProt
  Sequence type: Protein
  Keep MBits: T
  Maximum file size: 3000000000B

  HOSTNAME: ?
  SHELL: ?
  PWD: /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359
  PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/pdy23/.nextflow/assets/nf-core/funcscan/bin
  Progam name:  amrfinder_index
  Command line: /usr/local/bin/amrfinder_index amrfinderdb/2023-11-15.1/

  *** ERROR ***
  '/usr/local/bin/amrfinder_index' 'amrfinderdb/2023-11-15.1/' > /tmp/amrfinder_update.FoQYnY/amrfinder_index.err
  status = 256


  HOSTNAME: ?
  SHELL: ?
  PWD: /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359
  PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/pdy23/.nextflow/assets/nf-core/funcscan/bin
  Progam name:  amrfinder_update
  Command line: amrfinder_update -d amrfinderdb

Work dir:
  /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

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

executor >  local (40)
[d9/29f632] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[5a/67ad25] process > NFCORE_FUNCSCAN:FUNCSCAN:BI... [100%] 2 of 2 ✔
[ed/0e6003] process > NFCORE_FUNCSCAN:FUNCSCAN:PR... [100%] 2 of 2 ✔
[9f/edc837] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[d3/f90d15] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[77/d7b476] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[0f/eb4a0a] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[40/93a62d] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[19/cf0ff8] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[ee/aafa74] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[51/141f0f] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 1 of 1 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[f4/4a82ef] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[c8/300eca] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 4 of 4 ✔
[74/b034ce] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 8 of 8 ✔
[33/b78323] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[e3/a94b87] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 2 of 2 ✔
[82/de50f2] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:CU... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:MU... -

ERROR ~ Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update)'

Caused by:
  Process `NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update)` terminated with an error exit status (1)

Command executed:

  amrfinder_update -d amrfinderdb
  tar czvf amrfinderdb.tar.gz -C amrfinderdb/$(readlink amrfinderdb/latest) ./

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE":
      amrfinderplus: $(amrfinder --version)
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  Running: amrfinder_update -d amrfinderdb
  Looking up the published databases at https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/
  Looking for the target directory amrfinderdb/2023-11-15.1/
  Downloading AMRFinder database version 2023-11-15.1 into 'amrfinderdb/2023-11-15.1/'
  Running: /usr/local/bin/amrfinder_index amrfinderdb/2023-11-15.1/
  Indexing

  *** ERROR ***
  '/usr/local/bin/makeblastdb'  -in /tmp/amrfinder_index.Ylmgta/db/AMRProt  -dbtype prot  -logfile /tmp/amrfinder_index.Ylmgta/makeblastdb.AMRProt
  status = 135
  Building a new DB, current time: 01/03/2024 15:27:42
  New DB name:   /tmp/amrfinder_index.Ylmgta/db/AMRProt
  New DB title:  /tmp/amrfinder_index.Ylmgta/db/AMRProt
  Sequence type: Protein
  Keep MBits: T
  Maximum file size: 3000000000B

  HOSTNAME: ?
  SHELL: ?
  PWD: /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359
  PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/pdy23/.nextflow/assets/nf-core/funcscan/bin
  Progam name:  amrfinder_index
  Command line: /usr/local/bin/amrfinder_index amrfinderdb/2023-11-15.1/

  *** ERROR ***
  '/usr/local/bin/amrfinder_index' 'amrfinderdb/2023-11-15.1/' > /tmp/amrfinder_update.FoQYnY/amrfinder_index.err
  status = 256


  HOSTNAME: ?
  SHELL: ?
  PWD: /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359
  PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/pdy23/.nextflow/assets/nf-core/funcscan/bin
  Progam name:  amrfinder_update
  Command line: amrfinder_update -d amrfinderdb

Work dir:
  /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

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




executor >  local (40)
[d9/29f632] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[5a/67ad25] process > NFCORE_FUNCSCAN:FUNCSCAN:BI... [100%] 2 of 2 ✔
[ed/0e6003] process > NFCORE_FUNCSCAN:FUNCSCAN:PR... [100%] 2 of 2 ✔
[9f/edc837] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[d3/f90d15] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[77/d7b476] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[0f/eb4a0a] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[40/93a62d] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[19/cf0ff8] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [  0%] 0 of 2
[ee/aafa74] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[51/141f0f] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 1 of 1 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[f4/4a82ef] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[c8/300eca] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 4 of 4 ✔
[74/b034ce] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 8 of 8 ✔
[33/b78323] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[e3/a94b87] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 2 of 2 ✔
[82/de50f2] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:CU... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:MU... -
ERROR ~ Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update)'

Caused by:
  Process `NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update)` terminated with an error exit status (1)

Command executed:

  amrfinder_update -d amrfinderdb
  tar czvf amrfinderdb.tar.gz -C amrfinderdb/$(readlink amrfinderdb/latest) ./

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE":
      amrfinderplus: $(amrfinder --version)
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  Running: amrfinder_update -d amrfinderdb
  Looking up the published databases at https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/
  Looking for the target directory amrfinderdb/2023-11-15.1/
  Downloading AMRFinder database version 2023-11-15.1 into 'amrfinderdb/2023-11-15.1/'
  Running: /usr/local/bin/amrfinder_index amrfinderdb/2023-11-15.1/
  Indexing

  *** ERROR ***
  '/usr/local/bin/makeblastdb'  -in /tmp/amrfinder_index.Ylmgta/db/AMRProt  -dbtype prot  -logfile /tmp/amrfinder_index.Ylmgta/makeblastdb.AMRProt
  status = 135
  Building a new DB, current time: 01/03/2024 15:27:42
  New DB name:   /tmp/amrfinder_index.Ylmgta/db/AMRProt
  New DB title:  /tmp/amrfinder_index.Ylmgta/db/AMRProt
  Sequence type: Protein
  Keep MBits: T
  Maximum file size: 3000000000B

  HOSTNAME: ?
  SHELL: ?
  PWD: /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359
  PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/pdy23/.nextflow/assets/nf-core/funcscan/bin
  Progam name:  amrfinder_index
  Command line: /usr/local/bin/amrfinder_index amrfinderdb/2023-11-15.1/

  *** ERROR ***
  '/usr/local/bin/amrfinder_index' 'amrfinderdb/2023-11-15.1/' > /tmp/amrfinder_update.FoQYnY/amrfinder_index.err
  status = 256


  HOSTNAME: ?
  SHELL: ?
  PWD: /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359
  PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/pdy23/.nextflow/assets/nf-core/funcscan/bin
  Progam name:  amrfinder_update
  Command line: amrfinder_update -d amrfinderdb

Work dir:
  /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

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


executor >  local (40)
[d9/29f632] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[5a/67ad25] process > NFCORE_FUNCSCAN:FUNCSCAN:BI... [100%] 2 of 2 ✔
[ed/0e6003] process > NFCORE_FUNCSCAN:FUNCSCAN:PR... [100%] 2 of 2 ✔
[9f/edc837] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[d3/f90d15] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[77/d7b476] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[0f/eb4a0a] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[40/93a62d] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[19/cf0ff8] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [  0%] 0 of 2
[ee/aafa74] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[51/141f0f] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 1 of 1 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[f4/4a82ef] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[c8/300eca] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 4 of 4 ✔
[74/b034ce] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 8 of 8 ✔
[33/b78323] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[e3/a94b87] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 2 of 2 ✔
[82/de50f2] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:CU... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:MU... -
-[nf-core/funcscan] Sent summary e-mail to rodo@izw-berlin.de (sendmail)-
ERROR ~ Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update)'

Caused by:
  Process `NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update)` terminated with an error exit status (1)

Command executed:

  amrfinder_update -d amrfinderdb
  tar czvf amrfinderdb.tar.gz -C amrfinderdb/$(readlink amrfinderdb/latest) ./

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE":
      amrfinderplus: $(amrfinder --version)
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  Running: amrfinder_update -d amrfinderdb
  Looking up the published databases at https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/
  Looking for the target directory amrfinderdb/2023-11-15.1/
  Downloading AMRFinder database version 2023-11-15.1 into 'amrfinderdb/2023-11-15.1/'
  Running: /usr/local/bin/amrfinder_index amrfinderdb/2023-11-15.1/
  Indexing

  *** ERROR ***
  '/usr/local/bin/makeblastdb'  -in /tmp/amrfinder_index.Ylmgta/db/AMRProt  -dbtype prot  -logfile /tmp/amrfinder_index.Ylmgta/makeblastdb.AMRProt
  status = 135
  Building a new DB, current time: 01/03/2024 15:27:42
  New DB name:   /tmp/amrfinder_index.Ylmgta/db/AMRProt
  New DB title:  /tmp/amrfinder_index.Ylmgta/db/AMRProt
  Sequence type: Protein
  Keep MBits: T
  Maximum file size: 3000000000B

  HOSTNAME: ?
  SHELL: ?
  PWD: /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359
  PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/pdy23/.nextflow/assets/nf-core/funcscan/bin
  Progam name:  amrfinder_index
  Command line: /usr/local/bin/amrfinder_index amrfinderdb/2023-11-15.1/

  *** ERROR ***
  '/usr/local/bin/amrfinder_index' 'amrfinderdb/2023-11-15.1/' > /tmp/amrfinder_update.FoQYnY/amrfinder_index.err
  status = 256


  HOSTNAME: ?
  SHELL: ?
  PWD: /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359
  PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/pdy23/.nextflow/assets/nf-core/funcscan/bin
  Progam name:  amrfinder_update
  Command line: amrfinder_update -d amrfinderdb

Work dir:
  /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

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

executor >  local (40)
[d9/29f632] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[5a/67ad25] process > NFCORE_FUNCSCAN:FUNCSCAN:BI... [100%] 2 of 2 ✔
[ed/0e6003] process > NFCORE_FUNCSCAN:FUNCSCAN:PR... [100%] 2 of 2 ✔
[9f/edc837] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[d3/f90d15] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[77/d7b476] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[0f/eb4a0a] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[40/93a62d] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[19/cf0ff8] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [  0%] 0 of 2
[ee/aafa74] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[51/141f0f] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 1 of 1 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[f4/4a82ef] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[c8/300eca] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 4 of 4 ✔
[74/b034ce] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 8 of 8 ✔
[33/b78323] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[e3/a94b87] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 2 of 2 ✔
[82/de50f2] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:CU... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:MU... -
-[nf-core/funcscan] Sent summary e-mail to rodo@izw-berlin.de (sendmail)-
-[nf-core/funcscan] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update)'

Caused by:
  Process `NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update)` terminated with an error exit status (1)

Command executed:

  amrfinder_update -d amrfinderdb
  tar czvf amrfinderdb.tar.gz -C amrfinderdb/$(readlink amrfinderdb/latest) ./

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE":
      amrfinderplus: $(amrfinder --version)
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  Running: amrfinder_update -d amrfinderdb
  Looking up the published databases at https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/
  Looking for the target directory amrfinderdb/2023-11-15.1/
  Downloading AMRFinder database version 2023-11-15.1 into 'amrfinderdb/2023-11-15.1/'
  Running: /usr/local/bin/amrfinder_index amrfinderdb/2023-11-15.1/
  Indexing

  *** ERROR ***
  '/usr/local/bin/makeblastdb'  -in /tmp/amrfinder_index.Ylmgta/db/AMRProt  -dbtype prot  -logfile /tmp/amrfinder_index.Ylmgta/makeblastdb.AMRProt
  status = 135
  Building a new DB, current time: 01/03/2024 15:27:42
  New DB name:   /tmp/amrfinder_index.Ylmgta/db/AMRProt
  New DB title:  /tmp/amrfinder_index.Ylmgta/db/AMRProt
  Sequence type: Protein
  Keep MBits: T
  Maximum file size: 3000000000B

  HOSTNAME: ?
  SHELL: ?
  PWD: /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359
  PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/pdy23/.nextflow/assets/nf-core/funcscan/bin
  Progam name:  amrfinder_index
  Command line: /usr/local/bin/amrfinder_index amrfinderdb/2023-11-15.1/

  *** ERROR ***
  '/usr/local/bin/amrfinder_index' 'amrfinderdb/2023-11-15.1/' > /tmp/amrfinder_update.FoQYnY/amrfinder_index.err
  status = 256


  HOSTNAME: ?
  SHELL: ?
  PWD: /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359
  PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/pdy23/.nextflow/assets/nf-core/funcscan/bin
  Progam name:  amrfinder_update
  Command line: amrfinder_update -d amrfinderdb

Work dir:
  /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

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

executor >  local (40)
[d9/29f632] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[5a/67ad25] process > NFCORE_FUNCSCAN:FUNCSCAN:BI... [100%] 2 of 2 ✔
[ed/0e6003] process > NFCORE_FUNCSCAN:FUNCSCAN:PR... [100%] 2 of 2 ✔
[9f/edc837] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[d3/f90d15] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[77/d7b476] process > NFCORE_FUNCSCAN:FUNCSCAN:GU... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[0f/eb4a0a] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[40/93a62d] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[19/cf0ff8] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [  0%] 0 of 2
[ee/aafa74] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 2 of 2 ✔
[51/141f0f] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... [100%] 1 of 1 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AM... -
[f4/4a82ef] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[c8/300eca] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 4 of 4 ✔
[74/b034ce] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 8 of 8 ✔
[33/b78323] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[e3/a94b87] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 2 of 2 ✔
[82/de50f2] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [100%] 2 of 2 ✔
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:CU... -
[-        ] process > NFCORE_FUNCSCAN:FUNCSCAN:MU... -
-[nf-core/funcscan] Sent summary e-mail to rodo@izw-berlin.de (sendmail)-
-[nf-core/funcscan] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update)'

Caused by:
  Process `NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update)` terminated with an error exit status (1)

Command executed:

  amrfinder_update -d amrfinderdb
  tar czvf amrfinderdb.tar.gz -C amrfinderdb/$(readlink amrfinderdb/latest) ./

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE":
      amrfinderplus: $(amrfinder --version)
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  Running: amrfinder_update -d amrfinderdb
  Looking up the published databases at https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/
  Looking for the target directory amrfinderdb/2023-11-15.1/
  Downloading AMRFinder database version 2023-11-15.1 into 'amrfinderdb/2023-11-15.1/'
  Running: /usr/local/bin/amrfinder_index amrfinderdb/2023-11-15.1/
  Indexing

  *** ERROR ***
  '/usr/local/bin/makeblastdb'  -in /tmp/amrfinder_index.Ylmgta/db/AMRProt  -dbtype prot  -logfile /tmp/amrfinder_index.Ylmgta/makeblastdb.AMRProt
  status = 135
  Building a new DB, current time: 01/03/2024 15:27:42
  New DB name:   /tmp/amrfinder_index.Ylmgta/db/AMRProt
  New DB title:  /tmp/amrfinder_index.Ylmgta/db/AMRProt
  Sequence type: Protein
  Keep MBits: T
  Maximum file size: 3000000000B

  HOSTNAME: ?
  SHELL: ?
  PWD: /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359
  PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/pdy23/.nextflow/assets/nf-core/funcscan/bin
  Progam name:  amrfinder_index
  Command line: /usr/local/bin/amrfinder_index amrfinderdb/2023-11-15.1/

  *** ERROR ***
  '/usr/local/bin/amrfinder_index' 'amrfinderdb/2023-11-15.1/' > /tmp/amrfinder_update.FoQYnY/amrfinder_index.err
  status = 256


  HOSTNAME: ?
  SHELL: ?
  PWD: /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359
  PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/pdy23/.nextflow/assets/nf-core/funcscan/bin
  Progam name:  amrfinder_update
  Command line: amrfinder_update -d amrfinderdb

Work dir:
  /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/f4/4a82ef8d4cb1455589b9ef62258359

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

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

Relevant files

No response

System information

Nextflow version 23.10.0
HPC
Executor Slurm
Container engine: Singularity
OS Rocky Linux 8.9 (Green Obsidian)
Version of nf-core/funcscan: v1.1.4-g274042b
@pdy1084 pdy1084 added the bug Something isn't working label Jan 3, 2024
@jfy133
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jfy133 commented Jan 4, 2024

Ooof that looks like amrfinder itself borked for some reason... but it doesn't actually report the error message..

@jasmezz @Darcy220606 could you see if you fan replicate?

The other option @pdy1084 is to try downloading the database manually yourself and pass that to the pipeline. Pleas esee https://nf-co.re/funcscan/1.1.4/parameters#arg_amrfinderplus_db

@pdy1084
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pdy1084 commented Jan 4, 2024

Hi again @jfy133,

As you suggested, I have downloaded amrfinderplus_db to a folder, added the path to the nf-core parameters and run again the test. It seems that the error I get now is not related to AMRFINDERPLUS_UPDATE module anymore but instead to AMRFINDERPLUS_RUN. I checked and AMRprot is in the folder. Do you have any suggestions on how to address this?

Thank you!

----------------------- Run command

$ nextflow run nf-core/funcscan -r 1.1.4
--outdir /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/ -profile test,singularity
-params-file /mnt/beegfs/mnt/work/nf_core_funscan/nf-params_nfcore_test.json

----------------------- Here you can see nf-core/funcscan is reading well the database

...
AMP: AMPcombi
amp_ampcombi_cutoff : 0

ARG: AMRFinderPlus
arg_amrfinderplus_db : /mnt/beegfs/mnt/work/nf_core_funscan/databases/amrfinderplusdb

ARG: DeepARG
arg_skip_deeparg : true
...

------------------------ And here I post a chunk of the error message which keeps repeating:

[63/8e3b7a] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [ 0%] 0 of 4
[- ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[66/a4495c] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [ 0%] 0 of 2
[- ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[85/fcb015] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [ 0%] 0 of 2
[- ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[- ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... -
[- ] process > NFCORE_FUNCSCAN:FUNCSCAN:CU... -
[- ] process > NFCORE_FUNCSCAN:FUNCSCAN:MU... -
ERROR ~ Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_RUN (sample_2)'

Caused by:
Process NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_RUN (sample_2) terminated with an error exit status (1)

Command executed:

if [ "false" == "true" ]; then
gzip -c -d wastewater_metagenome_contigs_2.fasta > wastewater_metagenome_contigs_2.fasta
fi

if [ "false" == "true" ]; then
mkdir amrfinderdb
tar xzvf amrfinderplusdb -C amrfinderdb
else
mv amrfinderplusdb amrfinderdb
fi

amrfinder
-n wastewater_metagenome_contigs_2.fasta

--ident_min -1 --coverage_min 0.5 --translation_table 11
--database amrfinderdb
--threads 1 > sample_2.tsv

VER=$(amrfinder --version)
DBVER=$(echo $(amrfinder --database amrfinderdb --database_version 2> stdout) | rev | cut -f 1 -d ' ' | rev)

cat <<-END_VERSIONS > versions.yml
"NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_RUN":
amrfinderplus: $(amrfinder --version)
amrfinderplus-database: $(echo $(echo $(amrfinder --database amrfinderdb --database_version 2> stdout) | rev | cut -f 1 -d ' ' | rev))
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
Running: amrfinder -n wastewater_metagenome_contigs_2.fasta --ident_min -1 --coverage_min 0.5 --translation_table 11 --database amrfinderdb --threads 1
Software directory: '/usr/local/bin/'
Software version: 3.11.18
WARNING: This was compiled for running under bioconda, but $CONDA_PREFIX was not found
Reverting to hard coded directory: /opt/conda/conda-bld/ncbi-amrfinderplus_1691435906550/_build_env/share/amrfinderplus/data/latest
Database directory: '/mnt/beegfs/mnt/work/nf_core_funscan/databases/amrfinderplusdb'

*** ERROR ***
The BLAST database for AMRProt was not found. Use amrfinder -u to download and prepare database for AMRFinderPlus

HOSTNAME: ?
SHELL: ?
PWD: /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/51/a8e92627ade1063c88a5c46f99506d
PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/pdy23/.nextflow/assets/nf-core/funcscan/bin
Progam name: amrfinder
Command line: amrfinder -n wastewater_metagenome_contigs_2.fasta --ident_min -1 --coverage_min 0.5 --translation_table 11 --database amrfinderdb --threads 1

Work dir:
/mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/51/a8e92627ade1063c88a5c46f99506d

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

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

@jasmezz
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jasmezz commented Jan 11, 2024

Update: I could replicate it, the error seems only with the zipped DB version. Not solved yet, though...

@jfy133 jfy133 added this to the 1.2 - Brazilian Escondidinho milestone Jan 24, 2024
@jasmezz jasmezz mentioned this issue Apr 24, 2024
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@jasmezz
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jasmezz commented Apr 25, 2024

This should be solved now by #365

@jasmezz jasmezz closed this as completed Apr 25, 2024
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