Voila hanging during writing index

[Nicholas Webster]

Hi, I ran into a problem running voila view.  Voila seems to be installed OK, voila --help returns 

build % voila --help                                                                        

usage: voila [-h] [-v] [--license LICENSE] {tsv,view,modulize,filter,split,recombine,lr} ...

VOILA is a visualization package for Alternative Local Splicing Events.

positional arguments:

  {tsv,view,modulize,filter,split,recombine,lr}

    tsv                 Generate tsv output for the supplied files.

    view                Start service to view the visualization for the supplied files.

    modulize            Modulize splicing events and generate a breakdown of the modulization in multiple TSV files.

    filter              Make truncated versions of the input files of a more manageable file size for easier collaboration.

    split               Split classifier input dataset (splicegraph and voila files) into <N> equal parts, for the purpose of

                        running on a compute cluster

    recombine           Used to combine output from a `voila split` run, after all initial runs are complete

    lr                  Preprocess long read data from a variety of tools to append to the voila view visualization

options:

  -h, --help            show this help message and exit

  -v                    show program's version number and exit

  --license LICENSE

but when I use voila view on a deltas file it hangs:

build % voila view -j 1 -p 8000 splicegraph.sql Control-siTM7.deltapsi.voila

2025-04-03 11:23:49,124 (PID:95875) - INFO - Command: /opt/anaconda3/envs/majiq2/bin/voila view -j 1 -p 8000 splicegraph.sql Control-siTM7.deltapsi.voila

2025-04-03 11:23:49,124 (PID:95875) - INFO - Voila v2.5.10.dev1+ge7fb4fcc

2025-04-03 11:23:49,135 (PID:95875) - INFO - ╔═══════════════════════════════════════════════════════════════╗

2025-04-03 11:23:49,135 (PID:95875) - INFO - ╠╡ ACADEMIC License applied                                     ║

2025-04-03 11:23:49,135 (PID:95875) - INFO - ║  Name: Official Majiq Academic-only License                   ║

2025-04-03 11:23:49,135 (PID:95875) - INFO - ║  File: majiq_license_academic_official.lic.txt                ║

2025-04-03 11:23:49,135 (PID:95875) - INFO - ║  Expiration Date: Never                                       ║

2025-04-03 11:23:49,135 (PID:95875) - INFO - ║                                                               ║

2025-04-03 11:23:49,135 (PID:95875) - INFO - ╠╡ The academic license is for non-commercial purposes by       ║

2025-04-03 11:23:49,135 (PID:95875) - INFO - ╠╡ individuals at an academic or not for profit institution.    ║

2025-04-03 11:23:49,135 (PID:95875) - INFO - ╚═══════════════════════════════════════════════════════════════╝

2025-04-03 11:23:49,135 (PID:95875) - INFO - config file: /var/folders/9q/jtb1y2zn6dg5gw99h4x46vpc0000gn/T/tmp5hmbz8su

2025-04-03 11:23:49,151 (PID:95875) - INFO - Creating index: /Users/nicholaswebster/Roi/build/Control-siTM7.deltapsi.voila

2025-04-03 11:24:05,142 (PID:95875) - INFO - Writing index: /Users/nicholaswebster/Roi/build/Control-siTM7.deltapsi.voila

Serving on http://localhost:8000

If I run in debug it hangs at:

2025-04-03 13:13:18,011 (PID:96096) - DEBUG - Generating config object

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| [SETTINGS]

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| debug = True

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| disable_reads = False

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| enable_het_comparison_chooser = False

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| enable_type_indexing = False

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| force_index = False

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| host = 127.0.0.1

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| ignore_inconsistent_group_errors = False

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| memory_map_hdf5 = False

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| nproc = 7

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| num_web_workers = 7

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| parallel_chunksize = 0

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| port = 8000

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| preserve_handles_hdf5 = False

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| silent = False

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| splice_graph_only = False

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| strict_indexing = False

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| web_server = waitress

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| analysis_type = deltapsi

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| 

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| [FILES]

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| voila = /Users/nicholaswebster/Roi/build/Control-siTM7.deltapsi.voila

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| splice_graph = /Users/nicholaswebster/Roi/build/splicegraph.sql

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - CFG| 

2025-04-03 13:13:18,027 (PID:96096) - DEBUG - Generating config object

2025-04-03 13:13:18,027 (PID:96096) - INFO - Using index: /Users/nicholaswebster/Roi/build/Control-siTM7.deltapsi.voila

Serving on http://localhost:8000

Changing ports does not seem to have any effect.

I am running on Mac with OS 15.3.2 with python 3.10. in a virtual environment

Any idea where the issue might be?  Thanks Nick

[San Jewell]

Hi Nick,

The process "hanging" on the line "Serving on localhost:8000" is expected behavior. Voila view is a web server, so while it is running there you may open your web browser and navigate to localhost:8000 in order to view the app. Let me know if you are able to see results that way.

Thanks,

-San