Error in picard_collectmultiplemetrics about grenepipe HOT 4 CLOSED

Hi Brent,

that is near impossible to debug for me from the distance, and it might be in your data, and not in the pipeline. Hard to tell for now, and hence this will require some testing on your end. Here are some things you can try:

• You could check if you can run picard on these input files manually, and see if that works.
• You can try to run some other tools on these bam files (just some command from bamtools for example), to see if they find an error in the files as well.
• You can try to convert the file to sam an back to bam, or something like that, and see if this solves the issue.
• Lasty, you can also deactivate the rule, if you don't need these metrics. Simply comment out these lines.

Hope that helps, and let me know what you find :-)
Lucas

from grenepipe.

Hi @Brent-Saylor-Canopy, any news on this?

from grenepipe.

Hi, I've just turned it off so far

from grenepipe.

Haha I see, makes sense. Well, as I unfortunately cannot fix this without additional information, I'm going to close the issue for now, but feel free to re-open if you need this fixed at some point :-)

from grenepipe.