$ nextflow run fmalmeida/bacannot     --input bacannot_samplesheet.yaml     --output Resultadosilvestres     --bacannot_db ./bacannot_db_2023   --max_memory 100.GB    -profile docker 
N E X T F L O W  ~  version 23.04.1
Launching `https://github.com/fmalmeida/bacannot` [big_lamport] DSL2 - revision: 0798f3ce1e [master]


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  fmalmeida/bacannot v3.2
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Core Nextflow options
  revision       : master
  runName        : big_lamport
  containerEngine: docker
  launchDir      : /home/jfrancisco
  workDir        : /home/jfrancisco/work
  projectDir     : /home/jfrancisco/.nextflow/assets/fmalmeida/bacannot
  userName       : jfrancisco
  profile        : docker
  configFiles    : /home/jfrancisco/.nextflow/assets/fmalmeida/bacannot/nextflow.config

Input/output options
  input          : bacannot_samplesheet.yaml
  output         : Resultadosilvestres
  bacannot_db    : ./bacannot_db_2023

Max job request options
  max_memory     : 100.GB

!! Only displaying parameters that differ from the pipeline defaults !!
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If you use fmalmeida/bacannot for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.3627669

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

* Software dependencies
  https://github.com/fmalmeida/bacannot/blob/master/CITATIONS.md
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executor >  local (1687)
[-        ] process > BACANNOT:UNICYCLER                       -
[-        ] process > BACANNOT:FLYE                            -
[a1/448c55] process > BACANNOT:PROKKA (sample_2262)            [100%] 73 of 73 ✔
[2a/b5ccb5] process > BACANNOT:MLST (sample_2262)              [100%] 73 of 73 ✔
[27/4a09df] process > BACANNOT:BARRNAP (sample_2262)           [100%] 73 of 73 ✔
[6e/2d8836] process > BACANNOT:COMPUTE_GC (sample_2262)        [100%] 73 of 73 ✔
[70/1d73a2] process > BACANNOT:KOFAMSCAN (sample_2262)         [100%] 73 of 73 ✔
[e6/b6657d] process > BACANNOT:KEGG_DECODER (sample_2262)      [100%] 73 of 73 ✔
[08/6b5271] process > BACANNOT:PLASMIDFINDER (sample_2262)     [100%] 73 of 73 ✔
[07/496d95] process > BACANNOT:PLATON (sample_2262)            [100%] 73 of 73 ✔
[da/a90301] process > BACANNOT:ISLANDPATH (sample_2262)        [100%] 73 of 73 ✔
[f2/071924] process > BACANNOT:VFDB (sample_2262)              [100%] 73 of 73 ✔
[0e/8bc7f5] process > BACANNOT:VICTORS (sample_2262)           [100%] 73 of 73 ✔
[7e/b3f901] process > BACANNOT:PHAST (sample_2262)             [100%] 73 of 73 ✔
[85/27ae8e] process > BACANNOT:PHIGARO (sample_2262)           [100%] 73 of 73 ✔
[d7/916c42] process > BACANNOT:PHISPY (sample_2262)            [100%] 73 of 73 ✔
[41/79fa26] process > BACANNOT:ICEBERG (sample_2262)           [100%] 73 of 73 ✔
[63/004f99] process > BACANNOT:AMRFINDER (sample_2262)         [100%] 73 of 73 ✔
[02/91eff0] process > BACANNOT:CARD_RGI (sample_2262)          [100%] 73 of 73 ✔
[61/ec5110] process > BACANNOT:ARGMINER (sample_2262)          [100%] 73 of 73 ✔
[-        ] process > BACANNOT:RESFINDER                       -
executor >  local (1687)
[-        ] process > BACANNOT:UNICYCLER                       -
[-        ] process > BACANNOT:FLYE                            -
[a1/448c55] process > BACANNOT:PROKKA (sample_2262)            [100%] 73 of 73 ✔
[2a/b5ccb5] process > BACANNOT:MLST (sample_2262)              [100%] 73 of 73 ✔
[27/4a09df] process > BACANNOT:BARRNAP (sample_2262)           [100%] 73 of 73 ✔
[6e/2d8836] process > BACANNOT:COMPUTE_GC (sample_2262)        [100%] 73 of 73 ✔
[70/1d73a2] process > BACANNOT:KOFAMSCAN (sample_2262)         [100%] 73 of 73 ✔
[e6/b6657d] process > BACANNOT:KEGG_DECODER (sample_2262)      [100%] 73 of 73 ✔
[08/6b5271] process > BACANNOT:PLASMIDFINDER (sample_2262)     [100%] 73 of 73 ✔
[07/496d95] process > BACANNOT:PLATON (sample_2262)            [100%] 73 of 73 ✔
[da/a90301] process > BACANNOT:ISLANDPATH (sample_2262)        [100%] 73 of 73 ✔
[f2/071924] process > BACANNOT:VFDB (sample_2262)              [100%] 73 of 73 ✔
[0e/8bc7f5] process > BACANNOT:VICTORS (sample_2262)           [100%] 73 of 73 ✔
[7e/b3f901] process > BACANNOT:PHAST (sample_2262)             [100%] 73 of 73 ✔
[85/27ae8e] process > BACANNOT:PHIGARO (sample_2262)           [100%] 73 of 73 ✔
[d7/916c42] process > BACANNOT:PHISPY (sample_2262)            [100%] 73 of 73 ✔
[41/79fa26] process > BACANNOT:ICEBERG (sample_2262)           [100%] 73 of 73 ✔
[63/004f99] process > BACANNOT:AMRFINDER (sample_2262)         [100%] 73 of 73 ✔
[02/91eff0] process > BACANNOT:CARD_RGI (sample_2262)          [100%] 73 of 73 ✔
[61/ec5110] process > BACANNOT:ARGMINER (sample_2262)          [100%] 73 of 73 ✔
[-        ] process > BACANNOT:RESFINDER                       -
[-        ] process > BACANNOT:CALL_METHYLATION                -
[d5/04ae86] process > BACANNOT:REFSEQ_MASHER (sample_2262)     [100%] 73 of 73 ✔
[0c/ed95c8] process > BACANNOT:DIGIS (sample_2340)             [100%] 73 of 73 ✔
[42/e619d9] process > BACANNOT:ANTISMASH (sample_2262)         [100%] 73 of 73 ✔
[d5/578449] process > BACANNOT:SEQUENCESERVER (sample_2262)    [100%] 73 of 73 ✔
[89/c0fe76] process > BACANNOT:MERGE_ANNOTATIONS (sample_2262) [100%] 73 of 73 ✔
[54/ee598b] process > BACANNOT:DRAW_GIS (sample_139)           [  2%] 2 of 68
[94/c0c5ca] process > BACANNOT:GFF2GBK (sample_172)            [  4%] 3 of 68
[-        ] process > BACANNOT:CREATE_SQL                      [  0%] 0 of 68
[-        ] process > BACANNOT:JBROWSE                         -
[-        ] process > BACANNOT:REPORT                          -
[e1/96ee86] process > BACANNOT:SUMMARY (sample_160)            [  1%] 1 of 68, failed: 1
[-        ] process > BACANNOT:MERGE_SUMMARIES                 -
[4b/115153] process > BACANNOT:CIRCOS (sample_139)             [  2%] 2 of 68
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'BACANNOT:SUMMARY (sample_160)'

Caused by:
  Process `BACANNOT:SUMMARY (sample_160)` terminated with an error exit status (1)

Command executed:

  mkdir -p results/sample_160/annotation
  ln -rs annotation/* results/sample_160/annotation
  source activate falmeida-py
  falmeida-py bacannot2json -i results -o sample_160_summary.json

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "/opt/conda/envs/falmeida-py/bin/falmeida-py", line 33, in <module>
      sys.exit(load_entry_point('falmeida-py==1.0.0', 'console_scripts', 'falmeida-py')())
    File "/opt/conda/envs/falmeida-py/lib/python3.7/site-packages/falmeida_py/__main__.py", line 212, in main
      bacannot2json(args['--input'], args['--output'], args['--print'])
    File "/opt/conda/envs/falmeida-py/lib/python3.7/site-packages/falmeida_py/bacannot2json.py", line 107, in bacannot2json
      plasmids_stats( bacannot_summary )
    File "/opt/conda/envs/falmeida-py/lib/python3.7/site-packages/falmeida_py/plasmid_function.py", line 73, in plasmids_stats
      bacannot_summary[sample]['plasmid']['plasmidfinder']['meta']['database'] = results['Database'].unique().item()
  ValueError: can only convert an array of size 1 to a Python scalar

Work dir:
  /home/jfrancisco/work/e1/96ee86a42df4c84ef36c2bc0c22b82

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