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?