BWA-MEM not working

Is BWA-MEM not working?

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Hi @Mahadi_Hasan

The most current version of the BWA-MEM tool does not have any known issues when executed at the public Galaxy server

  • If you are working at, and you would like some help troubleshooting the problem, more information about the error or situation is needed.

    • If the job is “gray” in color, that means that it is queued. The server is very busy, and jobs can stay in the queued state for a few days, and potentially longer if you are running a large batch of jobs.
    • If the job is “red” in color, that means that it has errored. Sending in a bug report from the error dataset is one option – if you choose to do that, please include a link to this post in the bug report’s form “comments” section, then post back here you sent it in (so we know when to look for it). Be sure to not delete the inputs or outputs.
    • If you would rather troubleshoot publically, please post back either 1) a share link to the History and note the dataset number for the error result or 2) the full contents of the bug report form. The tool name, tool version, and the reported error message is a good place to start. Screenshots of the expanded error dataset and input datasets would also be very helpful.
  • If you are working at some other public Galaxy server, what is the URL? Or, are you working at your own Galaxy? Please clarify if this is your situation and we can follow-up more from there.

I added a few tags to your post that link to prior Q&A about troubleshooting, etc, but we can certainly help more directly.


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Update: There is a new issue with this tool at but it will be fixed very soon. Details in this post: BWA-MEM Index can't be found