Voila modulize freezing in some cases

[ЖИРАНДОЛЬ]

Hi everyone! 

I'm having some issues running voila (version 2.4.dev3+g85d07819) modulize mode.
I've successfully runed majiq build(version 2.4.dev3+g85d07819) , majiq deltapsi and get corect *.voila and *.tsv files. Commands were like:

deltapsi:
```majiq deltapsi -j 64 -o dpsi/ --minreads 5 -grp1 build/x1.fq.majiq build/x2.fq.majiq build/x3.fq.majiq build/x4.fq.majiq -grp2 build/x8.fq.majiq build/x5.fq.majiq build/x6.fq.majiq build/x7.fq.majiq -n E4_WT_KO_ E4_KO_hom```
modulize:
voila modulize -j 32 -d categorize/E4_WT_KO_-E4_KO_hom build/splicegraph.sql E4_WT_KO_-E4_KO_hom.deltapsi.voila --changing-between-group-dpsi 0.01 --non-changing-between-group-dpsi 0.01

i ran some comparisons in parallel, like cat batch_cmds | parallel 'eval {...}' (but, anyway, running commands not in parallel give me the same result)

But, in some cases, voila just freezes and when some batch commands are freezing in stage Processing Genes and Modules [55136/55359], and I got no data like cassette.tsv and other ouput of voila modulize.

last line of log file looks like:
2022-05-24 14:26:20,574 (PID:764828) - INFO - Writing TSVs to /path/to/folder

can you help me how to solve this issue? 


Best wishes,
Alex

[Paul Jewell]

Hi Alex,

This is very odd, and it a new issue, so you may need to help me with some debugging and explanation.

-Can you describe the environment and run conditions? Laptop or HPC, running over ssh? in a screen session? using a grid manager? locally?  What kind of machine and storage setup are you running on?

-When the command freezes, is their any activity still going on with the process? On Linux, for example, you can run the command '$ top' and check if there is still significant disk / CPU usage by the voila process at that time.

-Can you try a smaller run,  with and without multithreading?

   -for example, $ voila modulize -j 1 --debug-num-genes 100
                           $ voila modulize -j 1 --debug --debug-num-genes 100
                           $ voila modulize -j 2 --debug-num-genes 100

See if any of these complete without the freezing issue.

- It may also be that something is corrupt with the splicegraph/voila file when it gets to gene 55136. Are you able to run something like $ sha1sum splicegraph.sql  to verify that there are no I/O errors with these files?

Thanks.