Open chenjn11 opened 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:
<fn>
(...)Quitting from lines 227-234 (riboseqc_template.Rmd)
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:Quitting from lines 124-131 [fivepr_profiles] (riboseqc.rmd)
RiboseQC_analysis doesn't work and it seems that the .rmd file has some problems.