Question: Not able to run BWA
0
gravatar for snanda
7 months ago by
snanda0
snanda0 wrote:

I'm trying to run BWA-MEM using Galaxy. I have a reference.fastq (I built a custom reference) and reads.fastq.

I get an error " This is a new dataset and not all of its data are available yet". (though all the data are already all Galaxy)

bwa • 234 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by snanda0
0
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Grey colored datasets indicate that the job is in the queue. Allow it to stay there until processed. This might occur quickly or take up to about a day, depending on how many other jobs are queued/executing in your account and how busy the clusters are for that job type.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 7 months ago by Jennifer Hillman Jackson23k

Thank you.

It worked.

ADD REPLYlink written 7 months ago by snanda0
0
gravatar for snanda
7 months ago by
snanda0
snanda0 wrote:

I called variants using Mpileup. In the ALT column, what does <x> refer to?

Thanks

ADD COMMENTlink written 7 months ago by snanda0

A question similar to yours is posted here: https://biostar.usegalaxy.org/p/22190/

Please follow the same advice, including sending in a bug report if needed. That one is still being looked at, but if format/inputs are the issue, your solution may be a bit different.

Next time, please post new questions unrelated to the current post in a new post (instead of a comment with a new question). This helps the community to find open questions and reply with help.

Thanks! Jen

ADD REPLYlink written 7 months ago by Jennifer Hillman Jackson23k

Thank you.

I redid the analysis with the parameters speocfied in the post. No luck. I have sent the report to the Galaxy team.

ADD REPLYlink written 7 months ago by snanda0
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