Need help with "Map with BWA for Illumina" tool

Question: Need help with "Map with BWA for Illumina" tool

4.2 years ago by

morgane.moreau.info • 30

Australia

morgane.moreau.info • 30 wrote:

Hi,

I've been mapping this sample many times without any problem.

Now I'm trying to do the exact same thing and it doesn't work. It seems like it doesn't find the metadata.

I mapped 2 other samples at the same time as this one, the other 2 worked fine but not this one. Any idea why is that so ?

Thanks

Tool name: Map with BWA for Illumina
Tool version: 1.2.3
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/bwa_wrappers

map-with-bwa-for-illumina • 1.4k views

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modified 4.2 years ago • written 4.2 years ago by morgane.moreau.info • 30

If you get a red history output on main or test, you can submit an automated bug report which allows devteam members to check your history and help to find the source of the error and debug - assuming you don't mind us seeing your data.

Otherwise I doubt anyone can offer much of an answer without a lot more detail - like which Galaxy instance?

ADD REPLY • link modified 4.2 years ago • written 4.2 years ago by fubar ♦ 1.1k

4.2 years ago by

morgane.moreau.info • 30

Australia

morgane.moreau.info • 30 wrote:

It just stays gray in my History (I can't ask for a debug)

When I click on attributed it says

Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values.

and in the database/built, my custom built reference genome is no present, when I select it, it doesn't save it.

It is the simple mapping of 2 fastqsanger files using BWA. It worked fine before, I did the exact same thing with another 2 samples that I queued at the same time and the other 2 got mapped.

I'm stuck. I want to create a worflow and I need this data to be included.

ADD COMMENT • link written 4.2 years ago by morgane.moreau.info • 30

Hi, I'm just having the same problem just now. The first time the job was correctly added to the cue and stared running until I get the same message (Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values.)

I've tried to run the job again but it simply doesn't start and I don't know why. It simply stay grey and tell me that the job is waiting to run.

Did you find a way to solve the problem?

Thank you, it will be very helpfull to me.

ADD REPLY • link written 3.4 years ago by gponz • 0

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