Missing some output files for MultiQC

Question

[courtney.e.hershberger]

When I've run MultiQC in the past on RNA-Seq FastQC data, I've gotten 13 output files. Five of them are summary files that start with "multiqc_" (e.g. multiqc_fastqc.txt, MultiQC_general_stats), the other eight are the tables used to make the plots in the html output that start with "mqc_" (e.g. mqc_fastqc_sequence_length_distribution_plot_1.txt, Mac_fastqc_overrepresented_sequences_plot_1.txt). Recently when I've run MultiQC, I only get the five summary files (multiqc_data.json, multiqc_fastqc.txt, multiqc_general_stats.txt, multiqc_sources.txt, multiqc.log) and the other eight files are missing. My pipeline uses the content of some of "mqc_" tables to determine the next steps for data processing.

When I look at the log files from the successful run where I got all 13 files, the command was multiqc SRP1/fastqc -o SRP1/fastqc and the version was multiQC 1.9. When I do it again, with the same command using the same version of multiQC and the same Fastq files, I only get the 5 summary files. I've tried several versions of python (3.8.6, 3.7.3, 3.6.2) in case that was the problem, but it still isn't working. Looking a little deeper, I did change FastQC from version 0.11.9 to 0.11.7, but the output looks so similar. I have done a lot of googling and haven't found a solution.

[GenoMax]

Phil Ewels participates here but not frequently. You may want to post an issue on MultiQC GitHub to get his attention.

Edit: I just ran multiQC on a set of fastqc result files and only see 5 files in multiqc_data directory with v.1.10. Were you using a really old version of multiQC before?

[Phil Ewels]

I fixed my Biostars digest email earlier today! After several years of it being broken ;)

Answer 1

[Phil Ewels]

I can't remember when this changed, but I just had a play myself and it seems that you now need to use -p / --export (config export_plots) when you run MultiQC to get the plot data files.

[courtney.e.hershberger]

Success!!! When I read the documentation, I misinterpreted it, thinking that -p would create individual plots (like .jpg), not the data behind the plots. Thank you so much!