I have successfully called peaks on my bam files using earlier versions of MACS, however, in my first attempt at using MACS2 (using both the normal Galaxy instance and the Cistrome instance), I am getting fatal error messages when trying to use MACS2 callpeaks on my datasets. I have read in posts with errors similar to mine, that this could be due to the files not being aligned correctly. However, I have bam.bai outputs for both of my datasets, and have even successfully generated new ones using the IdxStats tool. Is is possible I need to merge these files in some way before running them through MACS2, or is there a Galaxy server error that could be causing this?
Any help would be much appreciated!