Cannot seem to find metrics files when using picard CollectMultipleMetrics

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1

Hi,

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.

Thanks!

2

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

3

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

Phil

5

Sure here’s an example:

NAME.CollectMultipleMetrics.rna_metrics.txt (2.9 KB)

6

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.

7

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.

Phil