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Question: MarkDuplicate on BWA reads getting paused
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gravatar for ssouravsingh12
3.4 years ago by
ssouravsingh12 • 0
ssouravsingh12 • 0 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
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modified 3.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.4 years ago by ssouravsingh12 • 0
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gravatar for Jennifer Hillman Jackson
3.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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
ADD COMMENT • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k
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