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lcalviell / Ribo-seQC

A comprehensive analysis tool for Ribo-seq and small RNA-seq data
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RiboseQC_analysis doesn't work #5

Open chenjn11 opened 1 month ago

chenjn11 commented 1 month ago

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 commented 1 month ago

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)
    1. knitr:::group_indices(grepl(begin, x), grepl(end, x), x, md)
    2. base::mapply(fun, chunk.begin, chunk.end, lines, seq_along(chunk.begin))
    3. knitr (local) <fn>(...)
    4. knitr:::match_chunk_end(pattern.end, line, i, b, lines)
    5. knitr (local) signal(...) Warning message: 10迭代仍没有聚合

Quitting from lines 227-234 (riboseqc_template.Rmd)