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.