HiCUP output if Tidyverse, Plotly and/or Pandoc not installed

[StevenWingett]

HiCUP does not give nice output if HTML summary reports are not generated owing to lack of Tidyverse, Plotly and/or Pandoc. Make this more elegant.

[cement-head]

Hi Steve,

Might be an error, might be just my install, got an error at the very end when running HiCUP 0.8.3 - seems the HTML version of the report wasn't generated. Attached is a screenshot of the output files, as well as a copy of the config file.  R is installed and the <tidyverse> & <plotly> packages are installed locally.  Running fully updated Ubuntu 18.04 LTS. Did I have to "start" R (via R Studio Server) and select (LOAD in the R environment, maybe?) the TIDYVERSE and PLOTLY packages manually ?

ERROR (from terminal)

---

$ perl hicup --config hicup_woodfrog.conf Starting HiCUP pipeline (v0.8.3) PLEASE NOTE: FROM VERSION 8, HICUP REQUIRES THE R PACKAGES TIDYVERSE AND PLOTLY INSTALLED SEE DOCUMENTATION FOR MORE DETAILS Detecting R automatically Found R at '/usr/bin/R' Reading genome digest file '/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/Digest_woodfrog_Sau3AI_None_09-09-39_24-05-2022.txt.gz' to determine Hi-C restriction enzyme Truncating with HiCUP Truncater v0.8.3 Truncating sequences at occurrence of sequences '[GATCGATC]' Truncating sequences Truncating /home/cbfgws6/Documents/HiC/Rsylv_ATCATGCG-AACAGTCC_L004_R1_001.fastq Truncating /home/cbfgws6/Documents/HiC/Rsylv_ATCATGCG-AACAGTCC_L004_R2_001.fastq Truncating complete Mapping with HiCUP Mapper v0.8.3 Using aligner 'bowtie2' Mapping /home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/Rsylv_ATCATGCG-AACAGTCC_L004_R1_001.trunc.fastq.gz Mapping /home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/Rsylv_ATCATGCG-AACAGTCC_L004_R2_001.trunc.fastq.gz Mapping complete Pairing files with HiCUP Mapper v0.8.3 Pairing Rsylv_ATCATGCG-AACAGTCC_L004_R1_001.map.sam and Rsylv_ATCATGCG-AACAGTCC_L004_R2_001.map.sam Pairing complete Filtering with HiCUP Filter v0.8.3 Processing digest file /home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/Digest_woodfrog_Sau3AI_None_09-09-39_24-05-2022.txt.gz Sonication protocol followed - Restriction_Enzyme1:Sau3AI [^GATC] Filtering /home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/Rsylv_ATCATGCG-AACAGTCC_L004_R1_2_001.pair.bam Filtering complete Removing duplicates with HiCUP Deduplicator v0.8.3 De-duplicating /home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/Rsylv_ATCATGCG-AACAGTCC_L004_R1_2_001.filt.bam De-duplication complete Creating combined HiCUP summary report Reading folder '/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf' Writing to: /home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/ 1 complete summary results groups identified in folder Created combined summary reports Could not generate HiCUP HTML summary report with run command 'R -e "rmarkdown::render('/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/r_scripts/hicup_reporter.rmd', params=list(summary_file='/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/Rsylv_ATCATGCG-AACAGTCC_L004_R1_2_001.hicup.bam.HiCUP_summary_report_tzTerrfGtH_15-53-50_24-05-2022.txt', ditag_lengths_file='/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/Rsylv_ATCATGCG-AACAGTCC_L004_R1_2_001.ditag_size_distribution_report.txt'), intermediates_dir='/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/', output_file='/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/Rsylv_ATCATGCG-AACAGTCC_L004_R1_2_001.hicup.bam.HiCUP_summary_report_tzTerrfGtH_15-53-50_24-05-2022.html')" > /dev/null 2>&1' Created HTML summary reports HiCUP processing complete.

hicup_woodfrog.conf.txt

[StevenWingett]

Hi,

Sorry to learn you are experiencing problems with HiCUP. It seems as though everything is complete, except the generation of the final summary report.

Just wondering, is Pandoc installed on your system?

Please try running the following command in the relevant folder. Is an error message written to the screen?

R -e "rmarkdown::render('/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/r_scripts/hicup_reporter.rmd', params=list(summary_file='/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/Rsylv_ATCATGCG-AACAGTCC_L004_R1_2_001.hicup.bam.HiCUP_summary_report_tzTerrfGtH_15-53-50_24-05-2022.txt', ditag_lengths_file='/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/Rsylv_ATCATGCG-AACAGTCC_L004_R1_2_001.ditag_size_distribution_report.txt'), intermediates_dir='/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/', output_file='/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/Rsylv_ATCATGCG-AACAGTCC_L004_R1_2_001.hicup.bam.HiCUP_summary_report_tzTerrfGtH_15-53-50_24-05-2022.html')"

Thanks, Steven

[cement-head]

Okay, well don't I feel stupid. Installed the Ubuntu package pandoc (as deb) on the system, and package pander in R, re-ran command. Got this:

$ R -e "rmarkdown::render('/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/r_scripts/hicup_reporter.rmd', params=list(summary_file='/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/Rsylv_ATCATGCG-AACAGTCC_L004_R1_2_001.hicup.bam.HiCUP_summary_report_tzTerrfGtH_15-53-50_24-05-2022.txt', ditag_lengths_file='/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/Rsylv_ATCATGCG-AACAGTCC_L004_R1_2_001.ditag_size_distribution_report.txt'), intermediates_dir='/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/', output_file='/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/Rsylv_ATCATGCG-AACAGTCC_L004_R1_2_001.hicup.bam.HiCUP_summary_report_tzTerrfGtH_15-53-50_24-05-2022.html')"

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> rmarkdown::render('/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/r_scripts/hicup_reporter.rmd', params=list(summary_file='/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/Rsylv_ATCATGCG-AACAGTCC_L004_R1_2_001.hicup.bam.HiCUP_summary_report_tzTerrfGtH_15-53-50_24-05-2022.txt', ditag_lengths_file='/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/Rsylv_ATCATGCG-AACAGTCC_L004_R1_2_001.ditag_size_distribution_report.txt'), intermediates_dir='/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/', output_file='/home/cbfgws6/Programs/HiCUP/HiCUP-0.8.3/wf/Rsylv_ATCATGCG-AACAGTCC_L004_R1_2_001.hicup.bam.HiCUP_summary_report_tzTerrfGtH_15-53-50_24-05-2022.html')

processing file: hicup_reporter.rmd
  |..                                                                    |   3%
  ordinary text without R code

  |.....                                                                 |   7%
label: setup (with options) 
List of 1
 $ include: logi FALSE

  |.......                                                               |  10%
  ordinary text without R code

  |..........                                                            |  14%
label: import_data (with options) 
List of 1
 $ echo: logi FALSE

Rows: 1 Columns: 39
── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr  (1): File
dbl (38): Total_Reads_1, Total_Reads_2, Not_Truncated_Reads_1, Not_Truncated...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
  |............                                                          |  17%
  ordinary text without R code

  |..............                                                        |  21%
label: truncation_mapping (with options) 
List of 1
 $ echo: logi FALSE

Joining, by = "Category"
Joining, by = "Category"
  |.................                                                     |  24%
  ordinary text without R code

  |...................                                                   |  28%
label: truncation_frequency (with options) 
List of 1
 $ echo: logi FALSE

  |......................                                                |  31%
  ordinary text without R code

  |........................                                              |  34%
label: truncation_length (with options) 
List of 1
 $ echo: logi FALSE

  |...........................                                           |  38%
  ordinary text without R code

  |.............................                                         |  41%
label: mapping_efficieny (with options) 
List of 1
 $ echo: logi FALSE

  |...............................                                       |  45%
  ordinary text without R code

  |..................................                                    |  48%
label: truncation_plot (with options) 
List of 1
 $ echo: logi FALSE

Quitting from lines 104-105 (hicup_reporter.rmd) 
Error in `check_required_aesthetics()`:
! geom_bar requires the following missing aesthetics: x and y
Backtrace:
 1. plotly::ggplotly(trunc_map_plot, tooltip = "Count")
 2. plotly:::ggplotly.ggplot(trunc_map_plot, tooltip = "Count")
 3. plotly::gg2list(...)
 4. plotly by_layer(function(l, d) l$compute_geom_1(d))
 5. plotly f(l = layers[[i]], d = data[[i]])
 6. l$compute_geom_1(d)
 7. ggplot2 f(..., self = self)
 8. ggplot2:::check_required_aesthetics(...)

Execution halted

[StevenWingett]

Ok. Just checking, do you have Pandoc installed?

If that is installed then I'm not sure of the problem. You could send me your text summary files and I'll try and run the reporter script on my system.

All the best, Steven

[StevenWingett]

Ah ok, re-read your message. So Pandoc is installed. Well, if you send me the summary text files I could try and run/debug this.

[7insong]

I encountered a similar issue when generating the HTML file at the end. I suggest that you disable this command ($command .= '> /dev/null 2>&1';) in the 'hicup_reporter' script to identify what went wrong with your process. In my situation, it indicated that my pandoc version is outdated and requires 3.1.12 or higher.

[StevenWingett]

Fair point, I'll redirect the output to a log file.