Question: Problem with Hisat2
gravatar for rptiluswatson
7 months ago by
rptiluswatson0 wrote:

Hi, I submitted a couple jobs for HiSAT2 but they have not been progressing over several hours. Is there a possible issue on my end or has anyone else been experiencing problems?

rna-seq alignment hisat2 bam • 252 views
ADD COMMENTlink modified 7 months ago by Jennifer Hillman Jackson25k • written 7 months ago by rptiluswatson0
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson25k wrote:


There are many paused jobs in your history (light blue in color). This means that there is a problem with the input(s).

I looked at just the first paused job (dataset 120) and the inputs are not paired fastqsanger reads -- instead, the same input (dataset 7) was selected for both the forward and reverse reads. Downstream jobs that have paused jobs used as inputs will automatically also become paused.

Troubleshooting help is in the Galaxy support FAQs:

Example analysis workflows are the Galaxy tutorials. I can see that your history is getting cluttered and that is probably leading to small usage errors like the one above -- I would strongly suggest learning about and using Dataset collections and tags to help keep things organized.

You'll need review each paused job to fix these types of problems and any others that may be present and then rerun. You don't need to send in a bug report for what is currently in your history - I've already reviewed the content.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 7 months ago • written 7 months ago by Jennifer Hillman Jackson25k
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