Problem with Viola view

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Jenny Empawi

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Mar 18, 2024, 5:13:21 AMMar 18
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Hello, I have about 356261 rows of delta psi output. How long does it take to run viola view? I tried multiple time with 8 cores and 8G each but the process stopped by itself without any error. 

San Jewell

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Mar 25, 2024, 1:05:46 PMMar 25
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Hi Jenny,

This can depend on multiple factors, though the biggest one is the number of voila files provided at once. Are you increasing the core count with -j8 ? The indexing process will only need to be run once on one set of files. There are two ways you can speed it up as well:

--skip-type-indexing will disable the types checkboxes on the index page but significantly speed up the indexing speed.
--memory-map-hdf5 will load the voila files into memory for processing which is a good option if you have the spare memory on your computer to support it. You'll also need to save the index file separately if you do this with --index-file <some path>

Let me know if any of these help, otherwise, feel free to post the screenshot of exactly what the output looks like so I may provide a mode detailed suggestion.

Thanks!
-San

Jenny Empawi

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Mar 26, 2024, 12:12:29 PMMar 26
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Hello San,
It worked! However, I have encounter key error when trying to view the output. 

I figured out the annotation file I am using has “gene:” in front of the gene_id that caused this issue. I compared to the example annotation file and found out it doesn’t have “gene:” in front. Would it be possible to change the name in splicegraph and deltapsi.voila instead of in annotation file and re-run it again?

 

Screenshot 2024-03-26 at 11.41.17 PM.png

Ref in example:

Screenshot 2024-03-26 at 11.55.37 PM.png

Ref that I used from ensemble:


Screenshot 2024-03-27 at 12.11.15 AM.png

Thank you for your help!

Best,
Jenny Empawi

San Jewell

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Mar 27, 2024, 9:32:12 AMMar 27
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Hi Jenny,

I am a bit confused here: the example ref names will only be used if you provide the example ref during build -- the program does not automatically insert the "gene:" prefix. (or remove it) The only way to generate splicegraph.sql with/without these strings is if the build was run with that reference file. It sort of sounds like something might be happening here where a majiq/voila file from one build was being used in view with splicegraph from another build.

Can you provide the commands that you use for the workflow? (build, deltapsi, view) so I can see if it looks like anything is amiss?

Thanks!
-San
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