Majiq V3 - splicegraph.zarr not compatible with voila lr

[Tom Cole]

Hello,

I'm having trouble getting voila lr to run as it won't accept my splicegraph input.

I constructed the splice graph with BAM files from the same experiment using Majiq v3. Here is the error message I receive below:

2025-07-21 14:50:04,129 (PID:1373104) - INFO - config file: /tmp/voila-config-4978eb8127e7a1d9eb49218837cf497c 2025-07-21 14:50:04,130 (PID:1373104) - INFO - Running LR 2025-07-21 14:50:04,130 (PID:1373104) - ERROR - unable to open database file Traceback (most recent call last): File "/home/tcole/.conda/envs/majiq_env/lib/python3.10/site-packages/rna_voila/run_voila.py", line 532, in main args.func() File "/home/tcole/.conda/envs/majiq_env/lib/python3.10/site-packages/rna_voila/longreads.py", line 211, in longReadsInputsToLongReadsVoila conn = sqlite3.connect(config.splice_graph_file) sqlite3.OperationalError: unable to open database file

[San Jewell]

Hi tjcole,

You are completely correct, the LR script slipped through the cracks in the port to majiq V3. I have made a minor version bump which covers this fix. Please run the same pip install command again to retrieve the latest version and let me know if that fixes the issue.

Thanks,

-San

[Tom Cole]

Thanks San,

I was also hoping to clarify next steps for downstream analysis. After obtaining the .lr.voila file, how does one perform categorization of the splice modules to obtain a breakdown of different event types?

Cheers,

Tom

[San Jewell]

Hi Tom,

At this point in time, "voila modulize" only works with majiq splicing detection, not long read modules. The long read data is only used for visualization and comparison with "voila view". That is, after using short read data for exploratory analysis, long reads can be integrated when drilling down on a small gene subset.  I can bring up a proposal to the lab for integration of voila LR with other voila modes besides view mode to see if there is a general desire for it.

Thanks,

-San

[Tom Cole]

Hi San,

Just to update you on how this is going, the issue has been fixed and voila lr now accepts the sg.zarr input.

Unfortunately I think voila modulize also might need an update to be compatible with majiq-v3. The error message i get when running voila modulize suggests that I need .sgc files to accompany my sg.zarr file. When i run majiq-v3 build the output is only the sg.zarr file. Are there any commands I can use to generate .sgc files?

Cheers,

Tom 

[San Jewell]

Hi Tom,

Yes, you will need sgc files which store the raw read counts. They are generated using "majiq-v3 sg-coverage" command. You can see this description in the lower part of the v3 code block on the migration page: https://biociphers.bitbucket.io/majiq-docs/v2-to-v3.html

Let me know if it helps!

-San