Related Q&A: Fasta format genome file in mirdeep2 (custom genome)
Hi @amir
If you used the built-in human genome hg38 for upstream steps, then you must also use that same genome in later steps. It is not built-in for the last tool. And human is very large, which can lead to errors due to exceeding resources. Both are explained in the prior post.
In short, there is either a mismatch between the genome/transcriptome used at each step, or the job is exceeding resources.
The human genome hg38 is sourced from UCSC. The version at Galaxy Main can be found here: http://datacache.galaxyproject.org/.
I think that Galaxy EU uses the same genome build/version/format, but I’ve pinged the EU admins below so they can confirm.
There isn’t a tutorial that uses these tools. The help is on the tool forms. The usual rules about mismatched inputs do apply for these tools and all others. See prior post for the link.
@hexylena @bjoern.gruening – Any more advice?
@amir It would be useful if you posted back the error message. You could also send that in as a bug report. You’ll get a copy of the bug report that include the stdout & stdin output (also available on the Job Details page – “i” icon in an expanded dataset).
Jobs that exceed resources can sometimes be due to input mismatches, and it looks as if that is your root issue (genome used for one step, transcriptome used for another), and that must be solved first.
Jobs that truely exceed resources, and not due to input problems, mean that you should set up your own Galaxy server where more resources can be allocated. Pretty sure you have those links but here they are again for others reading, or if you need a reminder:
- Troubleshooting resources for errors or unexpected results
- My job ended with an error. What can I do?
- Galaxy Choices summarized: https://galaxyproject.org/choices/
- All Choices: https://galaxyproject.org/use/
Thanks!