Cannot seem to find metrics files when using picard CollectMultipleMetrics


I’ve been collecting metrics using Picard “CollectMultipleMetrics” and using the output in multiqc. The report manages to process several of the input files, but not all. In particular, I have generated RnaSeqMetrics but they are not picked up.

The files are in the working directory, and as far as I can tell, they have the expected format. There’s no mention of anything in the logs (using -v)…so I’m a little stumped.

I’d appreciate a pointer to something I could look at to make multiqc notice the rna_seq metric files.


I should mention that I have not been using anything special in my configuration.yml

Hi @yfarjoun,

Please can you attach a file that doesn’t work as expected and we can take a look.

For reference, the test data that we currently have is here: test-data/data/modules/picard/RnaSeqMetrics at main · MultiQC/test-data · GitHub


Sure here’s an example:

NAME.CollectMultipleMetrics.rna_metrics.txt (2.9 KB)

I played around with this a little and it seems that the fact that I got this metric file from CollectMultipleMetrics, throws off MultiQC. Strangly enough, other metrics collected in the same manner are not affected, for example InsertSizeMetrics.

Thanks - Picard is a bit of a nightmare in that the output headers can be extremely variable. The search patterns need tweaking quite frequently as people find various combinations that don’t match. Can take a look, but based on your description this likely needs to be a GitHub issue with a code change to be honest.