RESULT_TSE exits with error

[kaanb93]

Description of the bug

Hello,

First of all, thank you for such program. I think it can be very very useful.

As I tried it with Docker, I ended up with the issue

Then, I tried it with Singularity. Here is the error code I'm getting.

Command used and terminal output

$ nextflow run deng-lab/viroprofiler --input sample_file.csv -profile singularity -c custom.config -params-file params.yml -r main

executor >  local (3)
[f8/92840d] process > VIROPROFILER:FASTQC (T2)                     [100%] 3 of 3, cached: 3 ✔
[1d/f67148] process > VIROPROFILER:FASTP (T2)                      [100%] 3 of 3, cached: 3 ✔
[82/7bff33] process > VIROPROFILER:SPADES (T3)                     [100%] 3 of 3, cached: 3 ✔
[c5/aaf9a8] process > VIROPROFILER:CONTIGLIB                       [100%] 1 of 1, cached: 1 ✔
[95/5e0d57] process > VIROPROFILER:CHECKV                          [100%] 1 of 1, cached: 1 ✔
[46/b3a605] process > VIROPROFILER:CONTIGLIB_CLUSTER               [100%] 1 of 1, cached: 1 ✔
[bc/17c08c] process > VIROPROFILER:GENEPRED4CTG                    [100%] 1 of 1, cached: 1 ✔
[c8/064604] process > VIROPROFILER:NRPROT                          [100%] 1 of 1, cached: 1 ✔
[05/665017] process > VIROPROFILER:NRGENE                          [100%] 1 of 1, cached: 1 ✔
[3c/71c014] process > VIROPROFILER:CONTIGINDEX                     [100%] 1 of 1, cached: 1 ✔
[b5/9f75e3] process > VIROPROFILER:MAPPING2CONTIGS2 (T2)           [100%] 3 of 3, cached: 3 ✔
[3e/7ba911] process > VIROPROFILER:ABUNDANCE                       [100%] 1 of 1, cached: 1 ✔
[41/2fbe56] process > VIROPROFILER:VIBRANT                         [100%] 1 of 1, cached: 1 ✔
[4f/de969a] process > VIROPROFILER:DVF                             [100%] 1 of 1, cached: 1 ✔
[0f/f9350b] process > VIROPROFILER:VIRCONTIGS_PRE                  [100%] 1 of 1, cached: 1 ✔
[23/f16a30] process > VIROPROFILER:VIRSORTER2                      [100%] 1 of 1, cached: 1 ✔
[05/ea29cc] process > VIROPROFILER:TAXONOMY_VCONTACT               [100%] 1 of 1, cached: 1 ✔
[3d/0c4563] process > VIROPROFILER:TAXONOMY_MMSEQS                 [100%] 1 of 1, cached: 1 ✔
[ca/661e1b] process > VIROPROFILER:TAXONOMY_MERGE                  [100%] 1 of 1, cached: 1 ✔
[c6/7cd84b] process > VIROPROFILER:BACPHLIP                        [100%] 1 of 1, cached: 1 ✔
[93/e6b594] process > VIROPROFILER:RESULTS_TSE                     [100%] 1 of 1, failed: 1 ✘
[05/65fbd2] process > VIROPROFILER:CUSTOM_DUMPSOFTWAREVERSIONS (1) [100%] 1 of 1 ✔
[26/e2439a] process > VIROPROFILER:MULTIQC                         [100%] 1 of 1 ✔
Execution cancelled -- Finishing pending tasks before exit
-[ViroProfiler] Pipeline completed with errors-
ERROR ~ Error executing process > 'VIROPROFILER:RESULTS_TSE'

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

Command executed:

  create_tse.r --fin_abcount abundance_contigs_count.tsv.gz \
               --fin_abtpm abundance_contigs_tpm.tsv.gz \
               --fin_abcov abundance_contigs_covered_fraction.tsv.gz \
               --fin_taxa taxa_mmseqs_formatted_all.tsv \
               --fin_checkv quality_summary.tsv \
               --fin_virsorter2 final-viral-score.tsv \
               --fin_vibrant VIBRANT_genome_quality_contigs.tsv \
               --fin_dvf dvf_virus.tsv \
               --fin_replicyc putative_vcontigs_pref1.fasta.bacphlip

Command exit status:
  1

Command output:
  (empty)

Command error:
  The following objects are masked from ‘package:matrixStats’:

      anyMissing, rowMedians

  Loading required package: Biostrings
  Loading required package: XVector

  Attaching package: ‘Biostrings’

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

      strsplit

  Error in `dplyr::left_join()`:
  ! Can't join `x$Contig` with `y$Contig` due to incompatible types.
  ℹ `x$Contig` is a <character>.
  ℹ `y$Contig` is a <logical>.
  Backtrace:
       ▆
    1. ├─vpfkit::create_vpftse(...)
    2. │ └─... %>% tibble::column_to_rownames("Contig")
    3. ├─tibble::column_to_rownames(., "Contig")
    4. │ ├─base::stopifnot(is.data.frame(.data))
    5. │ └─base::is.data.frame(.data)
    6. ├─dplyr::left_join(., df_replicyc, by = "Contig")
    7. ├─dplyr::left_join(., df_dvf, by = "Contig")
    8. ├─dplyr:::left_join.data.frame(., df_dvf, by = "Contig")
    9. │ └─dplyr:::join_mutate(...)
   10. │   └─dplyr:::join_cast_common(x_key, y_key, vars, error_call = error_call)
   11. │     ├─rlang::try_fetch(...)
   12. │     │ └─base::withCallingHandlers(...)
   13. │     └─vctrs::vec_ptype2(x, y, x_arg = "", y_arg = "", call = error_call)
   14. ├─vctrs (local) `<fn>`()
   15. │ └─vctrs::vec_default_ptype2(...)
   16. │   ├─base::withRestarts(...)
   17. │   │ └─base (local) withOneRestart(expr, restarts[[1L]])
   18. │   │   └─base (local) doWithOneRestart(return(expr), restart)
   19. │   └─vctrs::stop_incompatible_type(...)
   20. │     └─vctrs:::stop_incompatible(...)
   21. │       └─vctrs:::stop_vctrs(...)
   22. │         └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))
   23. │           └─rlang:::signal_abort(cnd, .file)
   24. │             └─base::signalCondition(cnd)
   25. └─rlang (local) `<fn>`(`<vctrs__2>`)
   26.   └─handlers[[1L]](cnd)
   27.     └─dplyr:::rethrow_error_join_incompatible_type(cnd, vars, error_call)
   28.       └─dplyr:::stop_join(...)
   29.         └─dplyr:::stop_dplyr(...)
   30.           └─rlang::abort(...)
  Execution halted

Relevant files

No response

System information

No response