Couldn't find any coverage file starting to run the bismark meth extractor ..

[bveyb]

Hello,

after running deduplicate, I did run Genome coverage & Sequencing depth.
I got the warning: WARNING: Genome (-g) files are ignored when BAM input is provided.

Now I run Bismark Methylation Extractor and got the
Note: Cytosine Calls (cx-reports) will start automatically after Methylation ExtractorCouldn't find any coverage file starting to run the bismark meth extractor ..

What is wrong, how to obtain a 'coverage file' and why is the sorted BAM file deleted after 'Genome coverage & Sequencing depth' is finished?

Thank you for help,
Olaf.