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nf-core / pixelator

Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
https://nf-co.re/pixelator
MIT License
8 stars 3 forks source link

Mac support for `nf-core-pixelator` #24

Closed ambarrio closed 1 year ago

ambarrio commented 1 year ago

Should we support Mac OS?

This is mine, still doesn't work: 


% nextflow run PixelgenTechnologies/nf-core-pixelator -r main -profile test,docker --testdata_root ../nf-core-pixelator-datasets
N E X T F L O W  ~  version 22.04.5
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [b80f30889b]
Launching `https://github.com/PixelgenTechnologies/nf-core-pixelator` [stupefied_pike] DSL2 - revision: c2f98772aa [main]

WARN: Found unexpected parameters:
* --publish_dir_mode: copy
* --report_name: report
* --percentile: 0.0
* --compute_coabundance: false
* --compute_colocalization: false
* --compute_polarization: false
* --cluster_min_count: 2
* --condition: optimal
* --big_clusters_recover: false
* --max_size_recover: 10000
* --max_size: null
* --min_size: null
* --use_counts: false
* --collapse_min_count: 1
* --collapse_mismatches: 2
* --neighbours: 60
* --umi2_end: null
* --umi2_start: null
* --umi1_end: null
* --umi1_start: null
* --upi2_end: null
* --upi2_start: null
* --upi1_end: null
* --upi1_start: null
* --algorithm: adjacency
* --demux_min_length: null
* --demux_mismatches: 0.1
* --pbs2: null
* --pbs1: null
* --mismatches: 0.1
* --remove_polyg: false
* --dedup: false
* --avg_qual: 20
* --max_n_bases: 3
* --min_length: null
* --max_length: null
* --trim_tail: 0
* --trim_front: 0
* --testdata_root: ../nf-core-pixelator-datasets
- Ignore this warning: params.schema_ignore_params = "publish_dir_mode,report_name,percentile,compute_coabundance,compute_colocalization,compute_polarization,cluster_min_count,condition,big_clusters_recover,max_size_recover,max_size,min_size,use_counts,collapse_min_count,collapse_mismatches,neighbours,umi2_end,umi2_start,umi1_end,umi1_start,upi2_end,upi2_start,upi1_end,upi1_start,algorithm,demux_min_length,demux_mismatches,pbs2,pbs1,mismatches,remove_polyg,dedup,avg_qual,max_n_bases,min_length,max_length,trim_tail,trim_front,testdata_root"

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/pixelator v0.1.0dev
------------------------------------------------------
Core Nextflow options
  revision                  : main
  runName                   : stupefied_pike
  containerEngine           : docker
  launchDir                 : /Users/ambarrio/WORK/IDEO/Colibri/Pixelgen_Technologies/src/nf-core-pixelator
  workDir                   : /Users/ambarrio/WORK/IDEO/Colibri/Pixelgen_Technologies/src/nf-core-pixelator/work
  projectDir                : /Users/ambarrio/.nextflow/assets/PixelgenTechnologies/nf-core-pixelator
  userName                  : ambarrio
  profile                   : test,docker
  configFiles               : /Users/ambarrio/.nextflow/assets/PixelgenTechnologies/nf-core-pixelator/nextflow.config, /Users/ambarrio/WORK/IDEO/Colibri/Pixelgen_Technologies/src/nf-core-pixelator/nextflow.config

Input/output options
  input                     : ../nf-core-pixelator-datasets/testdata/micro/test_samplesheet.csv

Reference genome options
  genome                    : R64-1-1
  fasta                     : s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

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

Generic options
  max_multiqc_email_size    : 2.MB

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

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

* Software dependencies
  https://github.com/nf-core/pixelator/blob/master/CITATIONS.md
------------------------------------------------------
executor >  local (1)
[2c/e83c80] process > NFCORE_PIXELATOR:PIXELATOR:INPUT_CHECK:SAMPLESHEET_CHECK (test_samplesheet.csv) [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_PIXELATOR:PIXELATOR:FASTQC                                               -
[-        ] process > NFCORE_PIXELATOR:PIXELATOR:CUSTOM_DUMPSOFTWAREVERSIONS                          -
[-        ] process > NFCORE_PIXELATOR:PIXELATOR:MULTIQC                                              [  0%] 0 of 1
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/pixelator] Pipeline completed with errors-
WARN: There's no process matching config selector: PIXELATOR.*
WARN: There's no process matching config selector: RENAME_READS
WARN: There's no process matching config selector: PIXELATOR_PREQC
WARN: There's no process matching config selector: PIXELATOR_ADAPTERQC
WARN: There's no process matching config selector: PIXELATOR_DEMUX
WARN: There's no process matching config selector: PIXELATOR_COLLAPSE
WARN: There's no process matching config selector: PIXELATOR_CLUSTER
Error executing process > 'NFCORE_PIXELATOR:PIXELATOR:INPUT_CHECK:SAMPLESHEET_CHECK (test_samplesheet.csv)'

Caused by:
  Process `NFCORE_PIXELATOR:PIXELATOR:INPUT_CHECK:SAMPLESHEET_CHECK (test_samplesheet.csv)` terminated with an error exit status (1)

Command executed:

  check_samplesheet.py \
      test_samplesheet.csv \
      samplesheet.valid.csv

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

Command exit status:
  1

Command output:
  ERROR: Please check samplesheet header -> sample,design,barcodes,fastq_1,fastq_2 != sample,fastq_1,fastq_2

Command error:
  WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested

Work dir:
  /Users/ambarrio/WORK/IDEO/Colibri/Pixelgen_Technologies/src/nf-core-pixelator/work/2c/e83c807c6ddc6596cbfea924b12a4a

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
fbdtemme commented 1 year ago

The pipeline seems outdated. Can you run: nextflow pull pixelgentechnologies/nf-core-pixelator

The nextflow run command will fetch the latest version of the pipeline when run for the first time, but after that you have to run the nextflow pull command to update. It will warn you though when a new version of the pipeline is available: NOTE: Your local project version looks outdated - a different revision is available in the remote repository [b80f30889b]

ambarrio commented 1 year ago

I did nextflow pull PixelgenTechnologies/nf-core-pixelator -r main and nextflow pull PixelgenTechnologies/nf-core-pixelator -r dev. That brought me the latest versions.

Then there was a problem with this:

% nextflow run PixelgenTechnologies/nf-core-pixelator -profile test,docker --testdata_root ../nf-core-pixelator-datasets -r main
N E X T F L O W  ~  version 22.04.5
Launching `https://github.com/PixelgenTechnologies/nf-core-pixelator` [furious_morse] DSL2 - revision: b80f30889b [main]

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/pixelator v0.1.0dev
------------------------------------------------------
Core Nextflow options
  revision                  : main
  runName                   : furious_morse
  containerEngine           : docker
  launchDir                 : /Users/ambarrio/WORK/IDEO/Colibri/Pixelgen_Technologies/src/nf-core-pixelator
  workDir                   : /Users/ambarrio/WORK/IDEO/Colibri/Pixelgen_Technologies/src/nf-core-pixelator/work
  projectDir                : /Users/ambarrio/.nextflow/assets/PixelgenTechnologies/nf-core-pixelator
  userName                  : ambarrio
  profile                   : test,docker
  configFiles               : /Users/ambarrio/.nextflow/assets/PixelgenTechnologies/nf-core-pixelator/nextflow.config, /Users/ambarrio/WORK/IDEO/Colibri/Pixelgen_Technologies/src/nf-core-pixelator/nextflow.config

Input/output options
  input                     : ../nf-core-pixelator-datasets/testdata/micro/test_samplesheet.csv

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

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

Generic options
  max_multiqc_email_size    : 2.MB
  testdata_root             : ../nf-core-pixelator-datasets

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

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

* Software dependencies
  https://github.com/nf-core/pixelator/blob/master/CITATIONS.md
------------------------------------------------------
executor >  local (12)
[4d/d1ce86] process > NFCORE_PIXELATOR:PIXELATOR:INPUT_CHECK:SAMPLESHEET_CHECK (test_samplesheet.csv) [100%] 1 of 1 ✔
[d1/7c0d98] process > NFCORE_PIXELATOR:PIXELATOR:RENAME_READS (test_data_1_T1)                        [100%] 2 of 2 ✔
[df/bfe274] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_CONCATENATE (test_data_1_T1)               [100%] 1 of 1 ✔
[f5/f9e0f9] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_PREQC (test_data_1_T1)                     [100%] 2 of 2 ✔
[fe/46b9f5] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_ADAPTERQC (test_data_1_T1)                 [100%] 2 of 2 ✔
[84/4d8362] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_DEMUX (test_data_1_T1)                     [100%] 2 of 2 ✔
[c0/ed1f63] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_COLLAPSE (test_data_1_T1)                  [  0%] 0 of 2
[-        ] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_CLUSTER                                    -
[-        ] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_REPORT                                     -
[-        ] process > NFCORE_PIXELATOR:PIXELATOR:CUSTOM_DUMPSOFTWAREVERSIONS                          -
Error executing process > 'NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_COLLAPSE (test_data_2_T1)'

Caused by:
  Process `NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_COLLAPSE (test_data_2_T1)` terminated with an error exit status (1)

Command executed:

  pixelator \
      --cores 2 \
      --log-file test_data_2_T1.pixelator-collapse.log \
      collapse \
      --samples "test_data_2_T1" \
      --output . \
      --design D12 \
      --algorithm adjacency         --neighbours 60 --mismatches 2 --min-count 1 \
      test_data_2_T1_R1.processed-CD14.fastq.gz test_data_2_T1_R1.processed-CD162.fastq.gz test_data_2_T1_R1.processed-CD19.fastq.gz test_data_2_T1_R1.processed-CD20.fastq.gz test_data_2_T1_R1.processed-CD26.fastq.gz test_data_2_T1_R1.processed-CD3.fastq.gz test_data_2_T1_R1.processed-CD4.fastq.gz test_data_2_T1_R1.processed-CD45.fastq.gz test_data_2_T1_R1.processed-CD45RA.fastq.gz test_data_2_T1_R1.proceexecutor >  local (12)
[4d/d1ce86] process > NFCORE_PIXELATOR:PIXELATOR:INPUT_CHECK:SAMPLESHEET_CHECK (test_samplesheet.csv) [100%] 1 of 1 ✔
[d1/7c0d98] process > NFCORE_PIXELATOR:PIXELATOR:RENAME_READS (test_data_1_T1)                        [100%] 2 of 2 ✔
[df/bfe274] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_CONCATENATE (test_data_1_T1)               [100%] 1 of 1 ✔
[f5/f9e0f9] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_PREQC (test_data_1_T1)                     [100%] 2 of 2 ✔
[fe/46b9f5] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_ADAPTERQC (test_data_1_T1)                 [100%] 2 of 2 ✔
[84/4d8362] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_DEMUX (test_data_1_T1)                     [100%] 2 of 2 ✔
[77/4c571f] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_COLLAPSE (test_data_2_T1)                  [ 50%] 1 of 2, failed: 1
[-        ] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_CLUSTER                                    -
[-        ] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_REPORT                                     -
[-        ] process > NFCORE_PIXELATOR:PIXELATOR:CUSTOM_DUMPSOFTWAREVERSIONS                          -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_COLLAPSE (test_data_2_T1)'

Caused by:
  Process `NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_COLLAPSE (test_data_2_T1)` terminated with an error exit status (1)

Command executed:

  pixelator \
      --cores 2 \
      --log-file test_data_2_T1.pixelator-collapse.log \
      collapse \
      --samples "test_data_2_T1" \
      --output . \
      --design D12 \
      --algorithm adjacency         --neighbours 60 --mismatches 2 --min-count 1 \
      test_data_2_T1_R1.processed-CD14.fastq.gz test_data_2_T1_R1.processed-CD162.fastq.gz test_data_2_T1_R1.processed-CD19.fastq.gz test_data_2_T1_R1.processed-CD20.fastq.gz test_data_2_T1_R1.processed-CD26.fastq.gz test_data_2_T1_R1.processed-CD3.fastq.gz test_data_2_T1_R1.processed-CD4.fastq.gz test_data_2_T1_R1.processed-CD45.fastq.gz test_data_2_T1_R1.processed-CD45RA.fastq.gz test_data_2_T1_R1.proceexecutor >  local (12)
[4d/d1ce86] process > NFCORE_PIXELATOR:PIXELATOR:INPUT_CHECK:SAMPLESHEET_CHECK (test_samplesheet.csv) [100%] 1 of 1 ✔
[d1/7c0d98] process > NFCORE_PIXELATOR:PIXELATOR:RENAME_READS (test_data_1_T1)                        [100%] 2 of 2 ✔
[df/bfe274] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_CONCATENATE (test_data_1_T1)               [100%] 1 of 1 ✔
[f5/f9e0f9] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_PREQC (test_data_1_T1)                     [100%] 2 of 2 ✔
[fe/46b9f5] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_ADAPTERQC (test_data_1_T1)                 [100%] 2 of 2 ✔
[84/4d8362] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_DEMUX (test_data_1_T1)                     [100%] 2 of 2 ✔
[c0/ed1f63] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_COLLAPSE (test_data_1_T1)                  [100%] 2 of 2, failed: 2 ✘
[-        ] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_CLUSTER                                    -
[-        ] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_REPORT                                     -
[-        ] process > NFCORE_PIXELATOR:PIXELATOR:CUSTOM_DUMPSOFTWAREVERSIONS                          -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_COLLAPSE (test_data_2_T1)'

Caused by:
  Process `NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_COLLAPSE (test_data_2_T1)` terminated with an error exit status (1)

Command executed:

  pixelator \
      --cores 2 \
      --log-file test_data_2_T1.pixelator-collapse.log \
      collapse \
      --samples "test_data_2_T1" \
      --output . \
      --design D12 \
      --algorithm adjacency         --neighbours 60 --mismatches 2 --min-count 1 \
      test_data_2_T1_R1.processed-CD14.fastq.gz test_data_2_T1_R1.processed-CD162.fastq.gz test_data_2_T1_R1.processed-CD19.fastq.gz test_data_2_T1_R1.processed-CD20.fastq.gz test_data_2_T1_R1.processed-CD26.fastq.gz test_data_2_T1_R1.processed-CD3.fastq.gz test_data_2_T1_R1.processed-CD4.fastq.gz test_data_2_T1_R1.processed-CD45.fastq.gz test_data_2_T1_R1.processed-CD45RA.fastq.gz test_data_2_T1_R1.processed-CD45RO.fastq.gz test_data_2_T1_R1.processed-CD62L.fastq.gz test_data_2_T1_R1.processed-CD63.fastq.gz test_data_2_T1_R1.processed-CD69.fastq.gz test_data_2_T1_R1.processed-CD7.fastq.gz test_data_2_T1_R1.processed-CD70.fastq.gz test_data_2_T1_R1.processed-CD72.fastq.gz test_data_2_T1_R1.processed-CD8.fastq.gz test_data_2_T1_R1.processed-CD82.fastq.gz test_data_2_T1_R1.processed-HLA-DR.fastq.gz test_datexecutor >  local (12)
[4d/d1ce86] process > NFCORE_PIXELATOR:PIXELATOR:INPUT_CHECK:SAMPLESHEET_CHECK (test_samplesheet.csv) [100%] 1 of 1 ✔
[d1/7c0d98] process > NFCORE_PIXELATOR:PIXELATOR:RENAME_READS (test_data_1_T1)                        [100%] 2 of 2 ✔
[df/bfe274] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_CONCATENATE (test_data_1_T1)               [100%] 1 of 1 ✔
[f5/f9e0f9] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_PREQC (test_data_1_T1)                     [100%] 2 of 2 ✔
[fe/46b9f5] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_ADAPTERQC (test_data_1_T1)                 [100%] 2 of 2 ✔
[84/4d8362] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_DEMUX (test_data_1_T1)                     [100%] 2 of 2 ✔
[c0/ed1f63] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_COLLAPSE (test_data_1_T1)                  [100%] 2 of 2, failed: 2 ✘
[-        ] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_CLUSTER                                    -
[-        ] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_REPORT                                     -
[-        ] process > NFCORE_PIXELATOR:PIXELATOR:CUSTOM_DUMPSOFTWAREVERSIONS                          -

Error executing process > 'NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_COLLAPSE (test_data_2_T1)'

Caused by:
  Process `NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_COLLAPSE (test_data_2_T1)` terminated with an error exit status (1)

Command executed:

  pixelator \
      --cores 2 \
      --log-file test_data_2_T1.pixelator-collapse.log \
      collapse \
      --samples "test_data_2_T1" \
      --output . \
      --design D12 \
      --algorithm adjacency         --neighbours 60 --mismatches 2 --min-count 1 \
      test_data_2_T1_R1.processed-CD14.fastq.gz test_data_2_T1_R1.processed-CD162.fastq.gz test_data_2_T1_R1.processed-CD19.fastq.gz test_data_2_T1_R1.processed-CD20.fastq.gz test_data_2_T1_R1.processed-CD26.fastq.gz test_data_2_T1_R1.processed-CD3.fastq.gz test_data_2_T1_R1.processed-CD4.fastq.gz test_data_2_T1_R1.processed-CD45.fastq.gz test_data_2_T1_R1.processed-CD45RA.fastq.gz test_data_2_T1_R1.processed-CD45RO.fastq.gz test_data_2_T1_R1.processed-CD62L.fastq.gz test_data_2_T1_R1.processed-CD63.fastq.gz test_data_2_T1_R1.processed-CD69.fastq.gz test_data_2_T1_R1.processed-CD7.fastq.gz test_data_2_T1_R1.processed-CD70.fastq.gz test_data_2_T1_R1.processed-CD72.fastq.gz test_data_2_T1_R1.processed-CD8.fastq.gz test_data_2_T1_R1.processed-CD82.fastq.gz test_data_2_T1_R1.processed-HLA-DR.fastq.gz test_data_2_T1_R1.processed-IgG1ctrl.fastq.gz test_data_2_T1_R1.processed-IsoT_ctrl.fastq.gz test_data_2_T1_R1.processed-hashtag.fastq.gz

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_COLLAPSE":
      pixelator: $(echo $(pixelator --version 2>&1) | sed 's/pixelator, version //g' )
  END_VERSIONS

Command exit status:
  1

Command output:
  Collapsing reads by antibody in sample test_data_2_T1

Command error:
  WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
  Traceback (most recent call last):
    File "/usr/local/bin/pixelator", line 6, in <module>
      sys.exit(main())
    File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1130, in __call__
      return self.main(*args, **kwargs)
    File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1055, in main
      rv = self.invoke(ctx)
    File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1657, in invoke
      return _process_result(sub_ctx.command.invoke(sub_ctx))
    File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
      return ctx.invoke(self.callback, **ctx.params)
    File "/usr/local/lib/python3.10/site-packages/click/core.py", line 760, in invoke
      return __callback(*args, **kwargs)
    File "/pixelator/pixelator/cli.py", line 119, in wrapper
      return func(*args, **kwargs)
    File "/pixelator/pixelator/cli.py", line 134, in wrapper
      return func(*args, **kwargs)
    File "/usr/local/lib/python3.10/site-packages/click/decorators.py", line 26, in new_func
      return f(get_current_context(), *args, **kwargs)
    File "/pixelator/pixelator/cli.py", line 1088, in collapse
      raise job.exception()
  concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.

Work dir:
  /Users/ambarrio/WORK/IDEO/Colibri/Pixelgen_Technologies/src/nf-core-pixelator/work/77/4c571f706cf9bf70939a690e687981

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

and there was a problem with collapse and how it handles the thread pool or the core pool I imagine.

But then, @fbdtemme fixed an armversion and everything worked.

% nextflow run . -profile test,docker --testdata_root ../nf-core-pixelator-datasets
N E X T F L O W  ~  version 22.04.5
Launching `./main.nf` [elegant_lalande] DSL2 - revision: d4a8567805

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/pixelator v0.1.0dev
------------------------------------------------------
Core Nextflow options
  runName                   : elegant_lalande
  containerEngine           : docker
  launchDir                 : /Users/ambarrio/WORK/IDEO/Colibri/Pixelgen_Technologies/src/nf-core-pixelator
  workDir                   : /Users/ambarrio/WORK/IDEO/Colibri/Pixelgen_Technologies/src/nf-core-pixelator/work
  projectDir                : /Users/ambarrio/WORK/IDEO/Colibri/Pixelgen_Technologies/src/nf-core-pixelator
  userName                  : ambarrio
  profile                   : test,docker
  configFiles               : /Users/ambarrio/WORK/IDEO/Colibri/Pixelgen_Technologies/src/nf-core-pixelator/nextflow.config

Input/output options
  input                     : ../nf-core-pixelator-datasets/testdata/micro/test_samplesheet.csv

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

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

Generic options
  max_multiqc_email_size    : 2.MB
  testdata_root             : ../nf-core-pixelator-datasets

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

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

* Software dependencies
  https://github.com/nf-core/pixelator/blob/master/CITATIONS.md
------------------------------------------------------
executor >  local (16)
[02/ddd670] process > NFCORE_PIXELATOR:PIXELATOR:INPUT_CHECK:SAMPLESHEET_CHECK (test_samplesheet.csv) [100%] 1 of 1 ✔
[ee/2484c2] process > NFCORE_PIXELATOR:PIXELATOR:RENAME_READS (test_data_2_T1)                        [100%] 2 of 2 ✔
[aa/b58103] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_CONCATENATE (test_data_1_T1)               [100%] 1 of 1 ✔
[f4/565eef] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_PREQC (test_data_1_T1)                     [100%] 2 of 2 ✔
[6a/79a443] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_ADAPTERQC (test_data_1_T1)                 [100%] 2 of 2 ✔
[7c/ef2e24] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_DEMUX (test_data_1_T1)                     [100%] 2 of 2 ✔
[d9/4ff3af] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_COLLAPSE (test_data_1_T1)                  [100%] 2 of 2 ✔
[db/15da9a] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_CLUSTER (test_data_1_T1)                   [100%] 2 of 2 ✔
[67/7a4877] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_REPORT (report)                            [100%] 1 of 1 ✔
[8d/7e79d5] process > NFCORE_PIXELATOR:PIXELATOR:CUSTOM_DUMPSOFTWAREVERSIONS (1)                      [100%] 1 of 1 ✔
-[nf-core/pixelator] Pipeline completed successfully-
Completed at: 26-Sep-2022 12:12:08
Duration    : 3m 34s
CPU hours   : 0.1
Succeeded   : 16

I am happily closing this! 🚀