Question: Need help with "Map with BWA for Illumina" tool
gravatar for christensentrine
3.6 years ago by
christensentrine10 wrote:

Thanks a lot for your answer. I  used FASTQ groomer to convert fastq format to fastqsanger. I started the mapping of my reads to the reference, without problems, however Galaxy does not reach the loading process. This gives me the message:

"A job has been successfully added to the queue - resulting in the following dataset:

58: Map with BWA for Illumina on data 51, data 49, and data 5: mapped reads

You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered."

But Galaxy does not end the task (even after waiting for more than an hour). Why is that? I have several mappings to perform and is a bit frustrated  about that I cannot accomplish even one. Hope anyone can help me with that issue.

Best regards, 

Trine Christensen


Tool name: Map with BWA for Illumina
Tool version: 1.2.3
Tool ID:
ToolShed URL:


map-with-bwa-for-illumina • 1.6k views
ADD COMMENTlink written 3.6 years ago by christensentrine10
gravatar for carlfeberhard
3.6 years ago by
United States
carlfeberhard390 wrote:

Hi, Trine

Is this on the Main, public Galaxy instance or one that is running locally for only you or your lab? 

What reference are you trying to align to and are you certain it's available on the Galaxy instance you're using?

BWA needs special index files for the reference genomes it aligns agains. You can check a reference availability by:

  1. Clicking the edit-attributes/pencil icon of your fasta file
  2. Clicking the 'Database / Build' drop down menu in the Edit Attributes page/center-panel
  3. Using the search field of the drop down to find your reference by name (for example, typing 'Zeb' will show all the available reference genomes that contain 'Zeb' - zebrafish, zebra finch, etc.)

If your genome isn't listed there, you'll need to talk to an administrator to add it.

Did the BWA run finally finish? Did it produce errors (a red dataset)?

Thanks for the info.

ADD COMMENTlink written 3.6 years ago by carlfeberhard390
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