RiboseQC_analysis doesn't work

[chenjn11]

RiboseQC_analysis(annotation_file='Mus_musculus.GRCm38.93.gtf_Rannot',

•               bam_files= "test/M12RPF-JC_A1-RPI37.rmRep.rmDup.sorted.bam",
  

•               write_tmp_files=F,readlength_choice_method="all", read_subset = F)
  

Loading annotation files in Mus_musculus.GRCm38.93.gtf_Rannot ... Sun Aug 11 23:24:52 2024
Loading annotation files --- Done! Sun Aug 11 23:24:55 2024
Extracting read lengths from test/M12RPF-JC_A1-RPI37.rmRep.rmDup.sorted.bam ... Sun Aug 11 23:24:59 2024
Extracting read lengths --- Done! Sun Aug 11 23:25:20 2024
Analyzing BAM file: test/M12RPF-JC_A1-RPI37.rmRep.rmDup.sorted.bam ... Sun Aug 11 23:25:20 2024
Analyzing BAM file --- Done! Sun Aug 11 23:29:46 2024
Building aggregate 5' profiles ... Sun Aug 11 23:29:48 2024
Building aggregate 5' profiles --- Done! Sun Aug 11 23:35:24 2024
Calculating P-sites offsets ... Sun Aug 11 23:35:24 2024
Calculating P-sites offsets --- Done! Sun Aug 11 23:35:27 2024
Calculating P-sites positions and junctions ... Sun Aug 11 23:35:27 2024
Calculating P-sites positions and junctions --- Done! Sun Aug 11 23:40:33 2024
Building aggregate P-sites profiles ... Sun Aug 11 23:40:33 2024
Building aggregate P-sites profiles --- Done! Sun Aug 11 23:44:08 2024
Exporting files ... Sun Aug 11 23:44:08 2024
Exporting files --- Done! Sun Aug 11 23:44:48 2024

Creating html report in test/M12RPF-JC_A1-RPI37.rmRep.rmDup.sorted.bam_RiboseQC_report.html ... Sun Aug 11 23:44:48 2024

processing file: riboseqc.rmd
|........ | 38% [fivepr_profiles] Error in data_profile[[3]]:
! 下标出界
Backtrace:

1. Ribo.seQC::plot_metagene_hm(...)
   Warning message:
   10迭代仍没有聚合

Quitting from lines 124-131 [fivepr_profiles] (riboseqc.rmd)

RiboseQC_analysis doesn't work and it seems that the .rmd file has some problems.

[chenjn11]

Loading annotation files in Mus_musculus.GRCm38.93.gtf_Rannot ... Mon Aug 12 00:02:35 2024
Loading annotation files --- Done! Mon Aug 12 00:02:37 2024
Extracting read lengths from test/M12RPF-JC_A1-RPI37.rmRep.rmDup.sorted.bam ... Mon Aug 12 00:02:40 2024
Extracting read lengths --- Done! Mon Aug 12 00:03:14 2024
Analyzing BAM file: test/M12RPF-JC_A1-RPI37.rmRep.rmDup.sorted.bam ... Mon Aug 12 00:03:14 2024
Analyzing BAM file --- Done! Mon Aug 12 00:07:37 2024
Building aggregate 5' profiles ... Mon Aug 12 00:07:38 2024
Building aggregate 5' profiles --- Done! Mon Aug 12 00:11:36 2024
Calculating P-sites offsets ... Mon Aug 12 00:11:36 2024
Calculating P-sites offsets --- Done! Mon Aug 12 00:11:38 2024
Calculating P-sites positions and junctions ... Mon Aug 12 00:11:39 2024
Calculating P-sites positions and junctions --- Done! Mon Aug 12 00:13:49 2024
Building aggregate P-sites profiles ... Mon Aug 12 00:13:49 2024
Building aggregate P-sites profiles --- Done! Mon Aug 12 00:16:42 2024
Exporting files ... Mon Aug 12 00:16:42 2024
Exporting files --- Done! Mon Aug 12 00:18:17 2024

Creating html report in test/M12RPF-JC_A1-RPI37.rmRep.rmDup.sorted.bam_RiboseQC_report.html ... Mon Aug 12 00:18:17 2024

processing file: riboseqc_template.Rmd
Error:
! The closing fence on line 11 (" ") in riboseqc_template.Rmd does not match the opening fence "" on line 3. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info.
Backtrace:

1. BiocGenerics::paste(knit(text = out), collapse = "\n")
2. knitr::knit(text = out)
3. knitr:::process_file(text, output)
4. knitr:::split_file(lines = text)
5. knitr:::divide_chunks(lines, chunk.begin, chunk.end, markdown_mode)
6. knitr:::group_indices(grepl(begin, x), grepl(end, x), x, md)
7. base::mapply(fun, chunk.begin, chunk.end, lines, seq_along(chunk.begin))
8. knitr (local) <fn>(...)
9. knitr:::match_chunk_end(pattern.end, line, i, b, lines)
10. knitr (local) signal(...)
    Warning message:
    10迭代仍没有聚合

Quitting from lines 227-234 (riboseqc_template.Rmd)