Hello, I have run 96 assemblies from 14 subjects (6 timepoints each), TCR and IGH separately (28 runs) using the nebnext_umi_tcr / nebnext_umi_bcr profiles. Four runs (3x IGH and 1x TCR) repeatedly fail during the collapse duplicates step for one of the samples:

executor >  local (8)
[fa/dd6f48] NFC…S:UNZIP_IGBLAST (unzip_db) | 1 of 1, cached: 1 ✔
[97/fcdf2a] NFC…REFERENCE_FASTA (unzip_db) | 1 of 1, cached: 1 ✔
[72/3c5cd6] NFC…PLESHEET_CHECK (6_TCR.tsv) | 1 of 1, cached: 1 ✔
[-        ] NFC…ASTQ_INPUT_CHECK:CAT_FASTQ -
[ff/c32613] NFC…LY:PRESTO_UMI:FASTP (s6_9) | 6 of 6, cached: 6 ✔
[ce/edc803] NFC…MI:RENAME_FASTQ_UMI (s6_3) | 6 of 6, cached: 6 ✔
[a1/b840d6] NFC…ESTO_UMI:GUNZIP_UMI (s6_3) | 6 of 6, cached: 6 ✔
[40/5c1d1b] NFC…RESTO_FILTERSEQ_UMI (s6_3) | 6 of 6, cached: 6 ✔
[5f/62a903] NFC…RIMERS_SCORE_UMI_R1 (s6_3) | 6 of 6, cached: 6 ✔
[f5/162249] NFC…RIMERS_SCORE_UMI_R2 (s6_9) | 6 of 6, cached: 6 ✔
[37/568098] NFC…:PRESTO_PAIRSEQ_UMI (s6_9) | 6 of 6, cached: 6 ✔
[58/42b283] NFC…BUILDCONSENSUS_UMI (s6_85) | 6 of 6, cached: 6 ✔
[3f/4e485d] NFC…SENSUS_PAIRSEQ_UMI (s6_85) | 6 of 6, cached: 6 ✔
[4e/95d967] NFC…LEPAIRS_SEQUENTIAL (s6_-5) | 6 of 6, cached: 6 ✔
[27/0074b3] NFC…C_POSTASSEMBLY_UMI (s6_-5) | 6 of 6, cached: 6 ✔
[73/b0c47c] NFC…ADERS_COLLAPSE_UMI (s6_-5) | 6 of 6, cached: 6 ✔
[d2/95d561] NFC…HEADERS_PRIMERS_UMI (s6_3) | 6 of 6, cached: 6 ✔
[66/3244ca] NFC…STO_COLLAPSESEQ_UMI (s6_3) | 6 of 6, cached: 6 ✔
[f5/216eac] NFC…EADERS_METADATA_UMI (s6_3) | 6 of 6, cached: 6 ✔
[df/0000ed] NFC…RESTO_SPLITSEQ_UMI (s6_85) | 6 of 6, cached: 6 ✔
[04/a10ec7] NFC…HANGEO_ASSIGNGENES (s6_85) | 6 of 6, cached: 6 ✔
[55/43a168] NFC…ION:CHANGEO_MAKEDB (s6_85) | 6 of 6, cached: 6 ✔
[86/089132] NFC…ION:FILTER_QUALITY (s6_85) | 6 of 6, cached: 6 ✔
[ba/314fdb] NFC…ANGEO_PARSEDB_SPLIT (s6_3) | 6 of 6, cached: 5 ✔
[43/fa442f] NFC…ILTER_JUNCTION_MOD3 (s6_3) | 6 of 6, cached: 5 ✔
[69/77eec2] NFC…ION:ADD_META_TO_TAB (s6_3) | 6 of 6, cached: 5 ✔
[42/e9ebc9] NFC…OLLAPSE_DUPLICATES (s6_85) | 5 of 6, cached: 4, retries: 3 ✘
[-        ] NFC…YSIS:DEFINE_CLONES_COMPUTE | 0 of 1
[79/10fc03] NFC…EPORTING:PARSE_LOGS (logs) | 1 of 1, cached: 1 ✔
Plus 6 more processes waiting for tasks…
ERROR ~ Error executing process > 'NFCORE_AIRRFLOW:AIRRFLOW:BULK_QC_AND_FILTER:COLLAPSE_DUPLICATES (s6_85)'

Caused by:
  Process `NFCORE_AIRRFLOW:AIRRFLOW:BULK_QC_AND_FILTER:COLLAPSE_DUPLICATES (s6_85)` terminated with an error exit status (1)


Command executed:

  echo "s6_85_meta-pass.tsv" > tabs.txt
      Rscript -e "enchantr::enchantr_report('collapse_duplicates', \
          report_params=list('input'='tabs.txt',\
          'collapseby'='sample_id',\
          'outdir'=getwd(),\
          'nproc'=28,\
          'outname'='s6_85',\
          'log'='s6_85_collapse_command_log'))"

      cp -r enchantr s6_85_collapse_report && rm -r enchantr

      echo "NFCORE_AIRRFLOW:AIRRFLOW:BULK_QC_AND_FILTER:COLLAPSE_DUPLICATES": > versions.yml
      Rscript -e "cat(paste0('  enchantr: ',packageVersion('enchantr'),'
  '))" >> versions.yml

Command exit status:
  1

Command output:
  1/20
  2/20 [global-options]
  3/20
  4/20 [input-parameters]
  5/20 [unnamed-chunk-1]
  6/20
  7/20 [unnamed-chunk-2]
  8/20
  9/20 [unnamed-chunk-3]
  10/20
  11/20 [unnamed-chunk-4]
  12/20
  13/20 [findDuplicates]

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred


  processing file: _main.Rmd
  1/20
  2/20 [global-options]
  3/20
  4/20 [input-parameters]
  5/20 [unnamed-chunk-1]
  6/20
  7/20 [unnamed-chunk-2]
  8/20
  9/20 [unnamed-chunk-3]
  10/20
  11/20 [unnamed-chunk-4]
  12/20
  13/20 [findDuplicates]
  Error in `{
      this_group <- group_idx[i]
      this_group_size <- sum(db_subset[["collapse_idx"]] == this_group)
      if (this_group_size == 1) {
        return(db_subset %>% filter(collapse_idx == this_group) %>% mutate(
          collapse_count = 1))
      }
      collapsed_db <- collapseDuplicates(db_subset %>% filter(collapse_idx ==
        this_group), id = id, seq = seq, text_fields = text_fields, num_fields = num_fields,
      seq_fields = seq_fields, add_count = add_count, ignore = ignore, sep = sep,
      dry = dry, verbose = verbose)
      collapsed_db %>% select(any_of(c(columns, "collapse_count",
        "finddups_row_idx")))
    }`:
  ! task 4576 failed - "argument is of length zero"
  Backtrace:
      x
   1. \-enchantr::findDuplicates(...)
   2.   +-dplyr::bind_rows(...)
   3.   | \-rlang::list2(...)
   4.   \-... %dopar% ...
   5.     \-e$fun(obj, substitute(ex), parent.frame(), e$data)
  Warning messages:
  1: replacing previous import 'data.table::first' by 'dplyr::first' when loading 'enchantr'
  2: replacing previous import 'data.table::last' by 'dplyr::last' when loading 'enchantr'
  3: replacing previous import 'data.table::between' by 'dplyr::between' when loading 'enchantr'

  Quitting from _main.Rmd:189-200 [findDuplicates]
  Execution halted

When inspecting the

_meta-pass.tsv

files of the failing samples I cannot find an obvious issue. Any suggestions?