StopIteration error / Problem with mutate() input low_quality

[TakacsBertalan]

I am trying to use the Sunbeam Report extension, as written in the Readme. But after running sunbeam run --configfile=sunbeam_config.yml --use-conda final_report I am getting the following message: `Running: snakemake --snakefile /media/data/Sunbeam/sunbeam-dev/Snakefile --configfile=/media/data/Sunbeam/sunbeam-dev/orr_mikrobiom/sunbeam_config.yml --use-conda final_report Found extension sbx_report in folder sbx_report Collecting host/contaminant genomes... done. Collecting target genomes... done. Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 1 Rules claiming more threads will be scaled down. Job counts: count jobs 1 final_report 1

[Fri Nov 13 13:39:15 2020] rule final_report: input: /media/data/Sunbeam/sunbeam-dev/orr_mikrobiom/sunbeam_output/qc/reports/fastqc_quality.tsv, /media/data/Sunbeam/sunbeam-dev/orr_mikrobiom/sunbeam_output/qc/reports/preprocess_summary.tsv, /media/data/Sunbeam/sunbeam-dev/orr_mikrobiom/sunbeam_output/classify/kraken/all_samples.tsv output: /media/data/Sunbeam/sunbeam-dev/orr_mikrobiom/sunbeam_output/reports/final_report.html jobid: 0

[Fri Nov 13 13:39:15 2020] Error in rule final_report: jobid: 0 output: /media/data/Sunbeam/sunbeam-dev/orr_mikrobiom/sunbeam_output/reports/final_report.html conda-env: /media/data/Sunbeam/sunbeam-dev/orr_mikrobiom/sunbeam_output/.snakemake/conda/210568ab

RuleException: StopIteration in line 11 of /media/data/Sunbeam/sunbeam-dev/extensions/sbx_report/sbx_report.rules. File "/media/data/Sunbeam/sunbeam-dev/extensions/sbx_report/sbx_report.rules", line 11, in __rule_final_report File "/home/deltagene/anaconda3/envs/sunbeam-dev/lib/python3.6/concurrent/futures/thread.py", line 56, in run Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /media/data/Sunbeam/.snakemake/log/2020-11-13T133914.865999.snakemake.log`

I didn't change anything in the files, and the required input files for the rule do exist. All the dependencies are installed. What could be the problem?

[TakacsBertalan]

Update: After I running dos2unix on all the files of the extensions, I got a different error message: Activating conda environment: /media/data/Sunbeam/sunbeam-dev/orr_mikrobiom/sunbeam_output/.snakemake/conda/643af35d summarise() regrouping output by 'Direction' (override with .groups argument) Quitting from lines 281-303 (tmppkoc7wxa.final_report.Rmd) Error: Problem with mutate() input low_quality. ✖ object 'fwd_only' not found ℹ Input low_quality is (fwd_only + rev_only + dropped)/input. Backtrace: █

1. ├─rmarkdown::render(...)
2. │ └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
3. │ └─knitr:::process_file(text, output)
4. │ ├─base::withCallingHandlers(...)
5. │ ├─knitr:::process_group(group)
6. │ └─knitr:::process_group.block(group)
7. │ └─knitr:::call_block(x)
8. │ └─knitr:::block_exec(params)
9. │ ├─knitr:::in_dir(...)
   10. │ └─knitr:::evaluate(...)
   11. │ └─evaluate::evaluate(...)
   12. │ └─evaluate:::evaluate_call(...)
   13. │ ├─evaluate:::timing_fn(...)
   14. │ ├─base:::handle(...)
   15. │ ├─base::withCallingHandlers(...)
   16. │ ├─base::withVisible(eval(expr, envir, enclos))
   17. │ └─base::eval(expr, envir, enclos)
   18. │ └─base::eval(expr, envir, enclos)
   19. ├─%>%(...)
   20. │ ├─base::withVisible(eval(quote(_fseq(_lhs)), env, env))
   21. │ └─base::eval(quote(_fseq(_lhs)), env, env)
   22. │ └─base::eval(quote(_fseq(_lhs)), env, env)
   23. │ └─_fseq(_lhs)
   24. │ └─magrittr::freduce(value, _function_list)
   25. │ └─function_list[i]
   26. │ ├─dplyr::mutate(., low_quality = (fwd_only + rev_only + dropped)/input)
   27. │ └─dplyr:::mutate.data.frame(...)
   28. │ └─dplyr:::mutate_cols(.data, ...)
   29. │ ├─base::withCallingHandlers(...)
   30. │ └─mask$eval_all_mutate(dots[[i]])
   31. └─base::.handleSimpleError(...)
   32. └─dplyr:::h(simpleError(msg, call)) Execution halted

Seems like there is a problem with the .Rmd file. What could cause it?