Hi,
I’ve successfully used MAF to FASTA a few times on a ~400Mb MAF file using the one species per line setting, it’s incredibly convenient!
However, it is now being terminated due to exceeding the maximum run time with no success upon repeated attempts.
Is there anything I can do to amend this?
Many thanks.
Welcome, @Alasdair_T
The job runtimes are fixed at UseGalaxy.org. That is for practical reasons at this public site and doesn’t by itself mean there is anything going wrong.
For really long running jobs, you can try at UseGalaxy.eu instead. Jobs will run there until they complete, or fail, or may never die for a really long time due to some problem with the query, or for asking the tool to do something it simply can’t (anywhere, not just on public Galaxy clusters!).
So, you can certainly try and see what happens. But maybe check your MAF content… and the query species term to make sure more is not going on. You can also share your history here for feedback if wanted. 
ps: I love those tools, too! Protocol 5 in our Using Galaxy to Perform Large-Scale Interactive Data Analyses (2012) walks through an example. Most should still be about the same, and you can ask me here about any of that content and the updated usage (first author 
).
Hope this helps!
Thank you for your help! Your paper was very informative.
I’ve moved the job over to the .eu site and its been running for a few days but with no luck yet.
My previous job (which worked) was exactly the same besides changing out one sequence, so I am lost as to why it’s not working.
Should the issue be with my MAF input file, do you have any advice on finding that out? I notice there are mentions of error and output files, but my jobs never seem to produce any.
Many thanks!
If the job is still executing with a yellow/orange dataset, let it complete. That’s the only way to get the complete job logs.
Once you get green (successful) or red (error) dataset(s), then you can examine the job logs using the i-info icon. Click to expland the different sections. You can also sometimes notice input or parameter conflicts on this view.
I’m not sure what you mean by changing out one sequence? One of the sequences in the MAF alignment? I guess that could introduce technical (if the formatting is off) issues, but could also add in scientific complexity if that layered in a bunch of new gaps. Those gaps shouldn’t add too much complexity for fasta extraction though. You can explain more about this part if you want.