Temporary outputs of big jobs

Hi there!

I am now testing our new tool: MOABS on usegalaxy.eu Since this is a tool with multiple steps and quite time-consuming, the job has been running for a few days and no output yet.

I wonder if there is a way to have a look at the current progress of my job (which module is running, temporary outputs, error message if any).

Thank you in advance!

Best,
Mutian

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If this is a workflow then you can simply show hidden for the history. If these are intermediate files generated by a single tool then you will need filesystem access to the working directory on the Galaxy server.

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Thanks for your reply.

Do you mind give me more education about how to access the filesystem of my working directory? I am testing the tool on the website interface.

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If you are not a system administrator of the server then you can’t.

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@jennaj

Thanks so much for your help with metilene.

I’m facing the same issue as @Henry_Zhang with MOABS tool jobs running for almost a week now.
I just want to make sure it’s all running well and hasn’t failed at the cluster.

Could you suggest.

Hi @akanksha_bafna

The job will eventually show up as a red failed dataset if something went wrong.

If you are working at the EU server, know that jobs will run for a runtime window. If the data is just large, that could be a valid runtime given the resources allocated at the cluster nodes. Or, it could be a a run-away job … but that will still eventually fail.

What you could try:

  1. Start up the job again, but leave the original running.
  2. Try inputting smaller data, and start that also up, leave other jobs running.

Maybe the original job is too large to process, and possibly not just in Galaxy but anywhere. Or, maybe the cluster node where the original job is running has some issue. Or, maybe this is the actual runtime.

Checking on executing jobs is non-trival for administrators, especially for complicated tools that run multiple processes all together. MOABS is such a tool – and isn’t even hosted at all servers due to the computational demands.

The EU chat might be able to help … they would need the “job API ID” found on the same view where the logs are located in the application. A link to the chat is on the homepage of the server. Please know that this type of request might also be simply delayed – much of the team is traveling to Australia for our upcoming GCC conference plus making final tunings for the new features that will be presented.

Hope one of these works out for you :slight_smile:

Dear @jennaj -
The job API : 11ac94870d0bb33afd7eccd72aeeae32
It is still running and has not ended.
On the homepage I could find links to Help<Support and not the Chat link.

Thanks ,
Akanksha

The chat link is at the very bottom of the UseGalaxy.eu homepage.