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Question: FASTQ groomer - problem with dataset?
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gravatar for ltosti88
3.2 years ago by
ltosti88 • 0
United Kingdom
ltosti88 • 0 wrote:

Hello,

I started running the FASTQ groomer tool on about 10 datasets in parallel, 2 days ago.

All of the jobs ran fine in about half an hour except one that is still running. Is this normal or is there a problem with this specific file?

Thanks for your help!

 
fastq groomer • 763 views
ADD COMMENT • link •
modified 3.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.2 years ago by ltosti88 • 0

Are you at https://usegalaxy.org?

If so that is unusually long. How big is the fastq file?

ADD REPLY • link modified 3.2 years ago • written 3.2 years ago by Martin Čech ♦♦ 4.9k

Yes, I'm on usegalaxy.org; the file is pretty big actually (3Gb) but the other nine ones were just a bit smaller...it sounds weird to me as well, but what should I do?

ADD REPLY • link written 3.2 years ago by ltosti88 • 0
1
gravatar for Jennifer Hillman Jackson
3.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Has the Groomer job completed by now? If not, then there is a problem. 3 GB is not very large when working on http://usegalaxy.org. Were you able to run other tools on this dataset, such as "FastQC"? This would be a simple test and could also provide some details about the dataset contents. 

Please send an update and if needed we can examine the dataset in your history, Thanks, Jen, Galaxy team
ADD COMMENT • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k
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