Hi, I’ve just had 2 samples fail at the

CRISPRSEQ_PLOTTER

stage (targeted pipeline,

-r 2.1.1

):

ERROR ~ Error executing process > 'NFCORE_CRISPRSEQ:CRISPRSEQ_TARGETED:CRISPRSEQ_PLOTTER (S06D7_XXX)'

Caused by:
  Essential container in task exited

Command executed:

  plotter.R \
      --cut_site=-3 \
      --indels_info=S06D7_XXX_indels.csv \
      --reference=S06D7_XXX_reference-correctOrient.fasta \
      --gRNA_sequence=GGGCTTAGAAAAAAGCTGGG \
      --sample_name=S06D7_XXX \
      --substitutions_info=S06D7_XXX_subs-perc.csv
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_CRISPRSEQ:CRISPRSEQ_TARGETED:CRISPRSEQ_PLOTTER":
      ggplot2: $(Rscript -e "cat(paste(packageVersion('ggplot2'), collapse='.'))")
      ShortRead: $(Rscript -e "cat(paste(packageVersion('ShortRead'), collapse='.'))")
      plyr: $(Rscript -e "cat(paste(packageVersion('plyr'), collapse='.'))")
      dplyr: $(Rscript -e "cat(paste(packageVersion('dplyr'), collapse='.'))")
      seqinr: $(Rscript -e "cat(paste(packageVersion('seqinr'), collapse='.'))")
      ggpubr: $(Rscript -e "cat(paste(packageVersion('ggpubr'), collapse='.'))")
      ggmsa: $(Rscript -e "cat(paste(packageVersion('ggmsa'), collapse='.'))")
      seqmagick: $(Rscript -e "cat(paste(packageVersion('seqmagick'), collapse='.'))")
      stringr: $(Rscript -e "cat(paste(packageVersion('stringr'), collapse='.'))")
      tidyr: $(Rscript -e "cat(paste(packageVersion('tidyr'), collapse='.'))")
      ggseqlogo: $(Rscript -e "cat(paste(packageVersion('ggseqlogo'), collapse='.'))")
      plotly: $(Rscript -e "cat(paste(packageVersion('plotly'), collapse='.'))")
      cowplot: $(Rscript -e "cat(paste(packageVersion('cowplot'), collapse='.'))")
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  (more omitted..)
    grid.draw.absoluteGrob  ggplot2
    grobHeight.absoluteGrob ggplot2
    grobWidth.absoluteGrob  ggplot2
    grobX.absoluteGrob      ggplot2
    grobY.absoluteGrob      ggplot2
  Attaching package: 'seqmagick'
  The following object is masked from 'package:seqinr':
      consensus
  Attaching package: 'tidyr'
  The following object is masked from 'package:S4Vectors':
      expand
  Attaching package: 'plotly'
  The following object is masked from 'package:XVector':
      slice
  The following object is masked from 'package:IRanges':
      slice
  The following object is masked from 'package:S4Vectors':
      rename
  The following objects are masked from 'package:plyr':
      arrange, mutate, rename, summarise
  The following object is masked from 'package:ggplot2':
      last_plot
  The following object is masked from 'package:stats':
      filter
  The following object is masked from 'package:graphics':
      layout
  Attaching package: 'cowplot'
  The following object is masked from 'package:ggpubr':
      get_legend
  `summarise()` has grouped output by 'Start', 'Length'. You can override using
  the `.groups` argument.
  Saving 7 x 7 in image
  `summarise()` has grouped output by 'Modification', 'Start', 'Length',
  'ins_nt'. You can override using the `.groups` argument.
  Error in if (s > 12 && (nchar(as.character(sread(ref_seq)[[1]])) > (s +  : 
    missing value where TRUE/FALSE needed
  In addition: Warning messages:
  1: The `<scale>` argument of `guides()` cannot be `FALSE`. Use "none" instead as
  of ggplot2 3.3.4.
  ℹ The deprecated feature was likely used in the ggseqlogo package.
    Please report the issue at <<https://github.com/omarwagih/ggseqlogo/issues>>. 
  2: In RColorBrewer::brewer.pal(N, "Set2") :
    minimal value for n is 3, returning requested palette with 3 different levels
  3: In RColorBrewer::brewer.pal(N, "Set2") :
    minimal value for n is 3, returning requested palette with 3 different levels
  4: In RColorBrewer::brewer.pal(N, "Set2") :
    minimal value for n is 3, returning requested palette with 3 different levels
  5: In RColorBrewer::brewer.pal(N, "Set2") :
    minimal value for n is 3, returning requested palette with 3 different levels
  Execution halted