Open dbajpp0 opened 2 years ago
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
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=$( cat input.1 ) cp /dades/jpp/bin/TransPi_Report_Ind.Rmd . Rscript -e "rmarkdown::render('TransPi_Report_Ind.Rmd',output_file='TransPiReport${sample_id}.html')" ${sample_id} false true false false false false
Command exit status: 1
Command output:
label: load_libraries (with options) List of 1 $ include: logi FALSE
label: readstats_table (with options) List of 1 $ echo: logi FALSE
label: qual_plot (with options) List of 1 $ echo: logi FALSE
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':
The following object is masked from 'package:stats':
The following object is masked from 'package:graphics':
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