Error rendering final report

[logankblair]

Pipeline errored out at final step:

  # Save version of quarto used
  cat <<-END_VERSIONS > versions.yml
  "PATHOGENSURVEILLANCE:MAIN_REPORT":
      quarto: $(quarto --version)
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
    installation as follows:
  
    $ sudo Rscript --vanilla -e 'install.packages("bspm", repos="https://cran.r-project.org")' 
  
  
  processing file: index.qmd
  1/69                         
  2/69 [knitr_settings]        
  3/69                         
  4/69 [load_libraries]        
  5/69                         
  6/69 [parse_inputs]          
  7/69                         
  8/69 [generate-tables]       
  9/69                         
  10/69 [simple-table]          
  11/69                         
  12/69 [unnamed-chunk-1]       
  13/69                         
  14/69 [detailed-groups-table] 
  15/69                         
  16/69 [unnamed-chunk-2]       
  17/69                         
  18/69 [detailed-samples-table]
  19/69                         
  20/69 [unnamed-chunk-3]       
  21/69                         
  22/69 [unnamed-chunk-4]       
  
  Quitting from lines  at lines 189-190 [unnamed-chunk-4] (index.qmd)
  Error in `[.data.frame`:
  ! undefined columns selected
  Backtrace:
   1. psminer::print_sample_metadata(sample_data)
   2. psminer:::print_static_table(...)
   5. base::`[.data.frame`(data, compressed_cols)
  Execution halted
  Warning message:
  D-Bus service not found!
  
  - If you are in a container environment, please consider adding the
    following to your configuration to silence this warning:
  
    options(bspm.sudo = TRUE)
  
  - If you are in a desktop/server environment, please remove any 'bspm'
    installation from the user library and force a new system
    installation as follows:
  
    $ sudo Rscript --vanilla -e 'install.packages("bspm", repos="https://cran.r-project.org")' 

Work dir:
  /home/buchananr/Desktop/pathogensurveillance/pathogen/work/ab/cb513f16d4a16b0fd241beebe21c36

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`

 -- Check '.nextflow.log' file for details

[zachary-foster]

What dataset produced this error?

[logankblair]

mycobacteroides_small.csv

[zachary-foster]

It working for me when I render it outside of the pipeline. Its probably an issue with the docker image. When is the last time you updated the pipeline? There was a change to the docker container last Friday.

[logankblair]

I think I updated it either Wednesday or Thursday last week. I'll try rerunning it now.

[masudermann]

I got a similar error to Logan (though not identical psminer specific error). I just pulled recent changes today. Everything else seemed to run without a hitch. The issue I had previously where no output was produced was resolved.

I get this error (for mixed_bacteria dataset).

Main command was:
nextflow run main.nf --input /home/marthasudermann/pathogensurveillance/test/data/metadata/mixed_bacteria.csv --outdir test_mixedbacteria2 --bakta_db /home/marthasudermann/Software/bakta_db_02_2024/db/ -profile docker -resume
My main error was what is pasted here:

ERROR ~ Error executing process > 'PATHOGENSURVEILLANCE:MAIN_REPORT (all)'

Caused by:
  Process `PATHOGENSURVEILLANCE:MAIN_REPORT (all)` terminated with an error exit status (1)

Command executed:

  # Copy source of report here cause quarto seems to want to make its output in the source
  cp -r --dereference main_report_template main_report
  
  # Render the report
  quarto render main_report \
      --output-dir all_report \
      -P inputs:../all_inputs
  
  # Rename outputs
  mv main_report/all_report/index.html all_pathsurveil_report.html
  mv main_report/all_report/index.pdf all_pathsurveil_report.pdf
  
  # Save version of quarto used
  cat <<-END_VERSIONS > versions.yml
  "PATHOGENSURVEILLANCE:MAIN_REPORT":
      quarto: $(quarto --version)
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  27/69                         
  28/69 [unnamed-chunk-7]       
  29/69                         
  30/69 [unnamed-chunk-8]       
  31/69                         
  32/69 [sketchtable]           
  33/69                         
  34/69 [unnamed-chunk-9]       
  35/69                         
  36/69 [ani_heatmap]           
  37/69                         
  38/69 [unnamed-chunk-10]      
  39/69                         
  40/69 [pocp_heatmap]          
  41/69                         
  42/69 [id_core_phylo]         
  43/69                         
  44/69 [unnamed-chunk-11]      
  45/69                         
  46/69 [unnamed-chunk-12]      
  47/69                         
  48/69 [parse_snp_trees]       
  49/69                         
  50/69 [plot_snp_trees]        
  51/69                         
  52/69 [unnamed-chunk-13]      
  53/69                         
  54/69 [div_no_snp_phylo]      
  55/69                         
  56/69 [parse_snp_align]       
  57/69                         
  58/69 [plot_msns]             
  
  Quitting from lines  at lines 431-467 [plot_msns] (index.qmd)
  Error in `print_figures_with_selector()`:
  ! could not find function "print_figures_with_selector"
  Execution halted
  Warning message:
  D-Bus service not found!
  
  - If you are in a container environment, please consider adding the
    following to your configuration to silence this warning:
  
    options(bspm.sudo = TRUE)
  
  - If you are in a desktop/server environment, please remove any 'bspm'
    installation from the user library and force a new system
    installation as follows:
  
    $ sudo Rscript --vanilla -e 'install.packages("bspm", repos="https://cran.r-project.org")' 

Work dir:
  /home/marthasudermann/pathogensurveillance/work/72/bc2f2922a86e880bb49765c398c545

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details

[masudermann]

My issue has now been resolved with the updated Docker container.

[logankblair]

As was mine!