error at TransPi_Report_Ind.Rmd

[dbajpp0]

I got this error at the final report. Could you give me some hint on how to solve it?

Cheers,
Joan

Something went wrong. Check error message below and/or log files.
Error executing process > 'get_report (1)'

Caused by:
Process get_report (1) terminated with an error exit status (1)

Command executed:

sample_id=$( cat input.1 )
cp /dades/jpp/bin/TransPi_Report_Ind.Rmd .
Rscript -e "rmarkdown::render('TransPi_Report_Ind.Rmd',output_file='TransPi_Report_${sample_id}.html')" ${sample_id} false true false false false false

Command exit status:
1

Command output:

|                                                                            
|.....                                                                 |   7%
ordinary text without R code


|                                                                            
|......                                                                |   9%

label: load_libraries (with options)
List of 1
$ include: logi FALSE

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|........                                                              |  11%
ordinary text without R code


|                                                                            
|.........                                                             |  13%

label: readstats_table (with options)
List of 1
$ echo: logi FALSE

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|...........                                                           |  15%
ordinary text without R code


|                                                                            
|............                                                          |  17%

label: qual_plot (with options)
List of 1
$ echo: logi FALSE

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|..............                                                        |  20%
ordinary text without R code


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|...............                                                       |  22%

label: qual_plot2 (with options)
List of 1
$ echo: logi FALSE

Command error:

processing file: TransPi_Report_Ind.Rmd

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

  last_plot

The following object is masked from 'package:stats':

  filter

The following object is masked from 'package:graphics':

  layout

Quitting from lines 87-100 (TransPi_Report_Ind.Rmd)
Error in 1:rqual[5, 1] : NA/NaN argument
Calls: ... withCallingHandlers -> withVisible -> eval -> eval -> plot_ly
Execution halted

Work dir:
/dades/jpp/TransPi/work/0b/979b0f5ca8ac4399d912ac57764e60

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

[rivera10]

Hello @dbajpp0,

It looks like the error is in the plot for the mean quality after filtering. Do you have in the directory /dades/jpp/TransPi/work/0b/979b0f5ca8ac4399d912ac57764e60 a file ending in _reads_qual.csv? If so, can you check is not empty? This file is needed for two plots in the report.

Best,
Ramón