Question: MarkDuplicate on BWA reads getting paused
gravatar for ssouravsingh12
3.4 years ago by
ssouravsingh120 wrote:

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.

bwa • 689 views
ADD COMMENTlink modified 3.4 years ago by Jennifer Hillman Jackson25k • written 3.4 years ago by ssouravsingh120
gravatar for Jennifer Hillman Jackson
3.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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, 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

ADD COMMENTlink written 3.4 years ago by Jennifer Hillman Jackson25k
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