Question: Not able to run BWA
0
gravatar for snanda
10 weeks 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 • 111 views
ADD COMMENTlink modified 9 weeks ago • written 10 weeks ago by snanda0
0
gravatar for Jennifer Hillman Jackson
10 weeks ago by
United States
Jennifer Hillman Jackson22k 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 10 weeks ago by Jennifer Hillman Jackson22k

Thank you.

It worked.

ADD REPLYlink written 9 weeks ago by snanda0
0
gravatar for snanda
9 weeks ago by
snanda0
snanda0 wrote:

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

Thanks

ADD COMMENTlink written 9 weeks 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 9 weeks ago by Jennifer Hillman Jackson22k

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 9 weeks ago by snanda0
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