Report failed

[fetyj]

Hi Felipe, Could you help with this issue I've got when running bacannot o my genomes, everything went just fine except the report step. I tried with my old genomes (which were successful at the time) and I get the same error with the last step (report).

Error executing process > 'BACANNOT:REPORT (S6272)'

Caused by:
  Process `BACANNOT:REPORT (S6272)` terminated with an error exit status (1)

Command executed:

  #!/usr/bin/env Rscript

  ## Copy reports
  system("cp /work/reports/* .") ;

  ## Remove empty files
  system("rm -f input.??") ;
  system("rm -f input.?") ;

  ## Generate generic Report
  rmarkdown::render("report_general.Rmd" ,   params = list( prokka  = "S6272.txt",                  kegg    = "S6272_kegg-decoder_heatmap_static.svg",                  barrnap = "S6272_rRNA.gff",                  mlst    = "S6272_mlst_analysis.txt",                  refseq_masher = "refseq_masher_results.txt",                  query = "S6272")) ;

  ## Generate Resistance Report
  rmarkdown::render("report_resistance.Rmd", params = list(    blast_id = 90 ,     blast_cov = 90,     amrfinder = "AMRFinder_resistance-only.tsv",     query = "S6272",     rgitool = "RGI_S6272.txt",     rgiparsed = "Parsed_RGI_S6272_hits.txt",     rgi_heatmap = "input.10",     argminer_blastp = "S6272_argminer_blastp_onGenes.summary.txt",     resfinder_tab = "input.12",     resfinder_pointfinder = "input.13",     resfinder_phenotype = "input.14",     gff = "S6272.gff")) ;

  ## Generate Virulence Report
  rmarkdown::render("report_virulence.Rmd" ,   params = list( blast_id = 90 ,                  blast_cov = 90,                  vfdb_blast = "S6272_vfdb_blastn_onGenes.txt",                  gff = "S6272.gff",                  victors_blast = "S6272_victors_blastp_onGenes.txt",                  query = "S6272")) ;

  ## Generate MGEs report
  rmarkdown::render("report_MGEs.Rmd",   params = list( blast_id = 85,                  blast_cov = 85,                  phigaro_dir = "/choppy/Bacteria_assembly/Lb_crispatus_S6272_bacannot/prophages/phigaro",                  phigaro_txt = "S6272_phigaro.tsv",                  phispy_tsv = "prophage.tsv",                  ice_prot_blast = "S6272_iceberg_blastp_onGenes.txt",                  ice_genome_blast = "S6272_iceberg_blastn_onGenome.summary.txt",                  plasmid_finder_tab = "results_tab.tsv",                  platon_tsv = "S6272.tsv",                  query = "S6272",                  gi_image = "teste.png",                  digis = "transposable_elements_digis.gff",                  gff = "S6272.gff",                  phast_prot_blast = "S6272_phast_blastp_onGenes.txt" )) ;

Command exit status:
  1

Command output:
  (empty)

Command error:
  Error in knit_params_get(input_lines, params) : 
    render params not declared in YAML: prokka
  Calls: <Anonymous> -> knit_params_get
  Execution halted

Work dir:
  /choppy/work/b4/6bf748098f0a65f87fc585bd51071a

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

Thanks,

Fety

[fmalmeida]

Hi @fetyj ,

thanks for using the pipeline. I think this is a simple error. In latest versions, I had to update the reports, so they can be compliant with bakta as well.

Unfortunately, when doing that, I just realised later that it broke previous v3.1 versions as they expect a different manner of rendering.

As I saw that after publishing, I still don’t know how to properly fix it. But I will surely work on that to make precious v3.1 versions compatible with available docker images.

But, if you use the latest versions of docker images and the pipeline itself, this error should not happen.

[fetyj]

Indeed, updating my version of the pipeline resolve the error. Thanks :)

Fety