I was trying to execute the MarkDuplicate on my BWA reads extracted from the dataset.The format of the dataset is FASTQ Illumina.When I try to execute the MarkDuplicate, My job gets paused in between; trying to resume the paused jobs does not work.I want to know if I am doing something wrong since I haven't used up my quota.
This tool is intended to be run on mapped fastq reads. This means that the input would be a BAM or SAM dataset that is coordinate sorted (use SortSam as needed).
If this is what you are already doing, double check the input job/dataset. Did it run successfully? Is the metadata OK? (a warning about metadata would appear at the top of the dataset if there is a problem).
Please let us know and if there is still a problem, we may ask you to share a history (with instructions about how, to keep it private and not on the forum). If you were not working on http://usegalaxy.org, please see if you can duplicate the issue there before sending in more information. If the problem is on a local, cloud, or another public server, the path to resolution can vary, so include details about where as needed.
Best, Jen, Galaxy team