ERROR ~ Error executing process > 'NFCORE_CRISPRSEQ:CRISPRSEQ_TARGETED:CIGAR_PARSER (S01A3_BSM)'

Caused by:
  Essential container in task exited

Command executed:

  cigar_parser.R \
      --cut_site=-3 \
      --input=S01A3_BSM.bam \
      --output=S01A3_BSM \
      --reference=S01A3_BSM_reference-correctOrient.fasta \
      --gRNA_sequence=GGTTACAGGATAGGCCTTCG \
      --sample_name=S01A3_BSM \
      --reference_template=\
      --template_bam=\
      --template= \
      --summary_file=S01A3_BSM_alignment_summary.csv \
  
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_CRISPRSEQ:CRISPRSEQ_TARGETED:CIGAR_PARSER":
      seqinr: $(Rscript -e "cat(paste(packageVersion('seqinr'), collapse='.'))")
      Rsamtools: $(Rscript -e "cat(paste(packageVersion('Rsamtools'), collapse='.'))")
      dplyr: $(Rscript -e "cat(paste(packageVersion('dplyr'), collapse='.'))")
      ShortRead: $(Rscript -e "cat(paste(packageVersion('ShortRead'), collapse='.'))")
      jsonlite: $(Rscript -e "cat(paste(packageVersion('jsonlite'), collapse='.'))")
      stringr: $(Rscript -e "cat(paste(packageVersion('stringr'), collapse='.'))")
      plotly: $(Rscript -e "cat(paste(packageVersion('plotly'), collapse='.'))")
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  (more omitted..)
      colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
      colWeightedMeans, colWeightedMedians, colWeightedSds,

.command.err

cat command.err 
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, <http://pmax.int|pmax.int>, pmin, <http://pmin.int|pmin.int>, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    expand.grid, I, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:seqinr':

    translate

The following object is masked from 'package:base':

    strsplit


Attaching package: 'dplyr'

The following objects are masked from 'package:Biostrings':

    collapse, intersect, setdiff, setequal, union

The following object is masked from 'package:XVector':

    slice

The following objects are masked from 'package:GenomicRanges':

    intersect, setdiff, union

The following object is masked from 'package:GenomeInfoDb':

    intersect

The following objects are masked from 'package:IRanges':

    collapse, desc, intersect, setdiff, slice, union

The following objects are masked from 'package:S4Vectors':

    first, intersect, rename, setdiff, setequal, union

The following objects are masked from 'package:BiocGenerics':

    combine, intersect, setdiff, union

The following object is masked from 'package:seqinr':

    count

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: BiocParallel
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following object is masked from 'package:dplyr':

    count

The following object is masked from 'package:seqinr':

    count


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'GenomicAlignments'

The following object is masked from 'package:dplyr':

    last


Attaching package: 'ShortRead'

The following object is masked from 'package:dplyr':

    id

Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

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 object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

`summarise()` has grouped output by 'pos'. You can override using the `.groups`
argument.
`summarise()` has grouped output by 'cigar'. You can override using the
`.groups` argument.
Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE,  : 
  arguments imply differing number of rows: 1, 0
Calls: rbind ... as.data.frame -> as.data.frame.list -> do.call -> <Anonymous>
In addition: Warning message:
In pick_filter(separated_indels) : NAs introduced by coercion
Execution halted