I tried to identify the repeats in the centromere region by chip-seq-mapper, but the output file of chip-seq mapper was empty.
Hi @ZCL
Where was the custom reference genome “contigs.fasta” sourced? Do you have a public link?
Which exact tool are you using, and the version? Find this at the very top of the tool form.
Also, what server are you working at? This one? UseGalaxy.cz - Galaxy Community Hub
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- Troubleshooting resources for errors or unexpected results
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If this is a data problem, we can probably solve that here. If it is some tool or resource problem, we can reach out to the server administrators for help.
Let’s start there 
Hi,
when you look at Tool Standard Error, you will see the cause…
the job has been killed due to exceeding allowed wall time limit.
Hi – I’m confused? Are @ZCL and @zsalvet the same person? I can help you to consolidate into one account if you want. Or you can have many here, it doesn’t matter. Let me know if you want help with this.
Otherwise, yes, a “wall time” error is possible. It means there is a problem with the inputs to fix (similar to memory failures), or that the job execution time exceeds what we’ve been able to allocate on the public server where you are working. Different servers have different execution limits, and this variable is usually fixed and can’t be changed (for technical reasons).
So, if you are sure that the data is Ok, for this type of message you could try at a different UseGalaxy server choice to see what happens. UseGalaxy.eu usually has the longest runtimes.
I’m still willing to troubleshoot data if that is needed by anyone. Some of these ChIP-seq tools are a bit complicated to use. We also have tutorials that cover the basic concepts, and starting here is a good place → Epigenetics / Tutorial List
Hi, I am one of CESNET/E-infra CZ admins, the ZCL’s job is in our old Galaxy server, my comment was reply to ZCL.
(Unfortunately, the job was considered succesful by Galaxy and it did not show
report button in UI, we will have to make directed problem reporting easier, our support e-mail for that server is regalaxy@rt.cesnet.cz)
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Oh hi @zsalvet Glad you are at the forum and thanks for clarifying what is going on.
@ZCL just to be clear, that email address is where you will be reporting any questions you may have when working at that server.
I’ve also included the UseGalaxy.cz in our troubleshooting guide at this forum for future questions: