Workflow fails at MSqRob step

Step to reproduce :

./nextflow run main.nf --raws "../../data/*.raw" --fasta "../../data/*.fasta" --miscleavages 2 --fragment_mass_tolerance 0.5 --precursor_mass_tolerance 10.0 --enzyme "Trypsin (no P rule)" --variable_mods "Acetylation of protein N-term" --experiment_design "../../data/pxd001819.txt" --max_cpus 16 --max_memory 59GB -profile docker -with-report -with-trace -with-timeline

Main error

  Error in `$<-.data.frame`(`*tmp*`, genotype, value = character(0)) :
    replacement has 0 rows, data has 27

Error log

Error executing process > 'run_msqrob (1)'

Caused by:
  Process `run_msqrob (1)` terminated with an error exit status (1)

Command executed:

  echo "raw_file        exp_condition   biorep" > none
  cp "pxd001819.txt" exp_design.txt
  mv "QuantifiedPeptides.tsv" q_input.txt
  mv "QuantifiedProteins.tsv" q_prot.txt
  Rscript /home/gelonch/dev/jupyterlab_root/wombatp/Compomics-Workflow/Nextflow/scripts/runMSqRob.R

Command exit status:
  1

Command output:
  (empty)

Command error:
  Loading required package: stats4

  Attaching package: ‘S4Vectors’

  The following objects are masked from ‘package:base’:

      expand.grid, I, unname

  Loading required package: ProtGenerics

  Attaching package: ‘ProtGenerics’

  The following object is masked from ‘package:stats’:

      smooth

executor >  local (112)
[dd/f52dc0] process > convert_raw_mzml (25)      [100%] 27 of 27 ✔
[b4/30bbf3] process > create_decoy_database (1)  [100%] 1 of 1 ✔
[d6/82feb9] process > create_searchgui_paramfile [100%] 1 of 1 ✔
[7f/efd8ad] process > run_searchgui_search (21)  [100%] 27 of 27 ✔
[f6/599bd6] process > run_peptideshaker (27)     [100%] 27 of 27 ✔
[73/366318] process > get_peptideshaker_tsv (24) [100%] 27 of 27 ✔
[8b/7e557c] process > flashLFQ_all               [100%] 1 of 1 ✔
[d9/d587ca] process > run_msqrob (1)             [100%] 1 of 1, failed: 1 ✘
[-        ] process > run_final_qc               -
Error executing process > 'run_msqrob (1)'

Caused by:
  Process `run_msqrob (1)` terminated with an error exit status (1)

Command executed:

  echo "raw_file        exp_condition   biorep" > none
  cp "pxd001819.txt" exp_design.txt
  mv "QuantifiedPeptides.tsv" q_input.txt
  mv "QuantifiedProteins.tsv" q_prot.txt
  Rscript /home/gelonch/dev/jupyterlab_root/wombatp/Compomics-Workflow/Nextflow/scripts/runMSqRob.R

Command exit status:
  1

Command output:
  (empty)

Command error:
  Loading required package: stats4

  Attaching package: ‘S4Vectors’

  The following objects are masked from ‘package:base’:

      expand.grid, I, unname

  Loading required package: ProtGenerics

  Attaching package: ‘ProtGenerics’

  The following object is masked from ‘package:stats’:

      smooth

  This is MSnbase version 2.20.0
    Visit https://lgatto.github.io/MSnbase/ to get started.

  Attaching package: ‘MSnbase’

  The following object is masked from ‘package:base’:

      trimws

  Loading required package: lme4
  Loading required package: Matrix

  Attaching package: ‘Matrix’

  The following object is masked from ‘package:S4Vectors’:

      expand

  Attaching package: ‘MSqRob’

  The following object is masked from ‘package:lme4’:

      getData

  Warning message:
  In options(stringsAsFactors = T) :
    'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
  Error in `$<-.data.frame`(`*tmp*`, genotype, value = character(0)) :
    replacement has 0 rows, data has 27
  Calls: $<- -> $<-.data.frame
  Execution halted

Work dir:
  /home/gelonch/dev/jupyterlab_root/wombatp/Compomics-Workflow/Nextflow/work/d9/d587caf90a1706fd49a8b2d8f73b71

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

wombat-p / Compomics-Workflow

Workflow fails at MSqRob step #17